Wanted to put this here to keep my notes in one spot (from another thread.)
I try to use the least amount of Retcons to tie it all together and borrow heavily from ideas that Tin_Man, Mytran and Albertese have put forth. As always, YMMV
Personal Theory (updated with regeneration theory):
The TOS Enterprise is mainly powered by dilithium crystals that are re-charged by it's matter/antimatter reactor system containing 3 reactor cores. The central M/AM reactor core charges the dilithium crystals which generates ("regenerates") antimatter fuel and simultaneously stores energy to be used to power ship's systems through the energizers. The regenerated AM is pumped to fuel the M/AM engines in the nacelles to generate the space warp. Unused M/AM fuel in the nacelles are stored there in temporary fuel pods and excess fuel is pumped back to the main fuel areas in the engineering hull.
It can be explained that all three reactor cores aren't involved in every episode. In "That Which Survives", Losira's sabotage of the engineering hull's M/AM core was enough to have a runaway ship. In "The Savage Curtain", the "red zone" alert could be something that only can happen in the nacelles since the aliens only needed to target
something that was vulnerable.
Notes
For example, there is plenty of evidence of a multiple matter-antimatter reactor model that indicates that there is a matter/antimatter reactor and fuel in each nacelle:
"The Doomsday Machine" - 35
WASHBURN: We made a complete check on structural and control damage, sir. As far as we can tell, something crashed through the deflectors and knocked out the generators. Somehow the antimatter in the warp drive pods has been deactivated.
Note: Evidence of antimatter in the warp drive pods aka nacelles.
SPOCK: I would say none, Captain. The energy generated by our power nacelles seems to attracts it. I doubt we could manoeuvre close enough without drawing a direct attack upon ourselves.
Note: Since the nacelles generate energy then it's a good chance they have a m/am reactor in them.
"The Apple" - 38
SCOTT: Scott, sir. Our antimatter pods are completely inert.
Note: Could the "antimatter pods" = the nacelles? Or is this specific to antimatter pod containing the antimatter fuel?
KIRK: Then use your imagination. Tie every ounce of power the ship has into the impulse engines. Discard the warp drive nacelles if you have to, and crack out of there with the main section, but get that ship out of there!
Note: Nothing specific to M/AM generation here other than the warp drive nacelles are weighing down the ship and they are trying to break out of orbit.
"Bread and Circuses" - 43
SPOCK: Portions of the antimatter nacelles, personal belongings. Captain, no signs of bodies whatsoever.
Note: More antimatter in the nacelles evidence.
"By Any Other Name" - 50
SPOCK: There is one other possibility, Mister Scott. The final decision, of course, must be the captain's, but I believe we must have it ready for him. The Enterprise is propelled by matter-anti-matter reactors. The barrier we must traverse is negative energy.
Note: An interesting clue. Multiple matter-antimatter reactors. Perhaps the three reactors spoken of in "Catspaw" (two for each nacelles and one for the engineering hull?) or just two (one for each nacelle)?
SCOTT: I have opened the control valves to the matter-anti-matter nacelles. On your signal, I will flood them with positive energy.
Note: "Matter-antimatter nacelles" - Yes
But what is this? Flood the nacelles with positive energy?
"The Savage Curtain" - 77
SCOTT: I can't explain it, sir, but the matter and antimatter are in red zone proximity.
KIRK: What caused that?
SCOTT: There's no knowing and there's no stopping it either. The shielding is breaking down. I estimate four hours before it goes completely. Four hours before the ship blows up.
...
KIRK: Scotty, inform Starfleet Command. Disengage nacelles, Jettison if possible. Mister Spock, assist them. Advise and analyse. Scotty? Scotty?
Note: Further evidence that there is matter and antimatter (and it happens to include the fuel) up in the nacelles. And this occurs very late in the production too... episode 77 no less. Interestingly, the Matter is also in the Red Zone? This may point to fuel in only specific locations can go into Red Zone which would explain how Kirk knew that only the nacelles were in trouble.
"Errand of Mercy" - 27
SPOCK: Minor, Captain. We were most fortunate. Blast damage in decks ten and eleven, minor buckling in the antimatter pods, casualties very light.
Note: "Antimatter pods" could mean the nacelles or just the pods in the nacelles or antimatter pods located somewhere else...
"Metamorphosis" - 31
SPOCK: Helm does not answer, Captain.
KIRK: Neither do the pods. Communications are dead. Building overload. Cut all power relays.
...
SULU: Steady. No, Mister Scott, bearing three ten mark thirty five just cleared. No antimatter residue.
SCOTT: All scanners, spherical sweep. Range, maximum. They'll have to pick it up.
Note: This is shuttlecraft-related but this also hints that those were antimatter pods and thus a warp powered shuttle.
"I, Mudd" - 41
NORMAN: I am in total control of your ship. I have connected the matter-antimatter pods to the main navigational bank. A trigger relay is now in operation. Any attempts to alter course will result in immediate destruction of this vessel.
Note: The pods word again 
but then we also have evidence for a single matter/antimatter reactor
"That Which Survives" - 69
SCOTT: Watkins, check the bypass valve on the matter/antimatter reaction chamber. Make sure it's not overheating.
WATKINS: But, Mister Scott, the board shows correct.
SCOTT: I didn't ask you to check the board, lad.
Note: Scotty indicates only one m/am reaction chamber (not multiples).
LOSIRA: Show me this unit. I wish to learn.
WATKINS: This is the matter-antimatter integrator control. That's the cut off switch.
LOSIRA: Not correct. That is the emergency overload bypass, which engages almost instantaneously. A wise precaution, considering it takes the antimatter longer to explode once the magnetic flow fails. I am for you, Mister Watkins.
WATKINS: Mister Scott, there's a strange woman who knows the entire plan of the Enterprise.
Note: A single overload bypass. Not multiple (at least two) if the m/am reactors were in the nacelles.
SCOTT: Aye, Mister Spock, and I found out why. The emergency bypass control of the matter-antimatter integrator is fused.
SCOTT: It's completely useless. The engines are running wild. There's no way to get at them. We should reach maximum overload in about fifteen minutes.
Note: Interestingly, Scotty couldn't just disengage the dilithium circuits/energisers and just cut the power to the warp engines. Perhaps if he did, then all that m/am energy has no where to go and well... boom! The M/AM engines in the nacelles are acting as the release valves until everything overloads...
SPOCK: As I recall the pattern of our fuel flow, there is an access tube leading to the matter-antimatter reaction chamber.
SCOTT: There's a service crawlway, but it's not meant to be used while the integrator operates.
SPOCK: Still, it is there, and it might be possible to shut off the fuel at that point.
SCOTT: What with? Bare hands?
SPOCK: A magnetic probe.
SCOTT: Any matter that comes in contact with antimatter triggers the explosion. And I'm not even sure a man can live in the crawlway in the energy stream of the magnetic field that bottles up the antimatter.
Note: Only one m/am reaction chamber mentioned here. And there appears to be only one place to shut off the antimatter fuel flow to it which doesn't match up with two nacelles with matter/antimatter reactors and their own antimatter fuel. Scotty would need to make a clone of himself if he were up in two different nacelles. Also, the service crawlway room wouldn't fit in the nacelle with the hallway outside.
and then some wiggle room to consider the possibility that the matter/antimatter reactor system consists of 3 reactor cores or chambers (1 in each nacelle and 1 in the engineering hull) that can be used individually or all together:
"Catspaw" - 30
DESALLE: Keep it up, Mister Chekov. Channel the entire output of reactors one, two, and three into the relay stations. Whatever it is, it's starting to weaken.
Note: Could indicate three matter/antimatter reactors.
"Galileo Seven" - 14
SCOTT: I can adjust the main reactor to function with a substitute fuel supply.
Note: This could mimic a 3 reactor setup for the Enterprise - a "main reactor" in the hull and one in each nacelle.
"Elaan of Troyius" - 57
SCOTT: The anti-matter pods are rigged to blow up the moment we go into warp drive.
...
SCOTT: I've got bad news, Captain. The entire dilithium crystal converter assembly is fused. No chance of repair.
SCOTT: It's completely unusable.
KIRK: No chance of restoring warp drive?
SCOTT: Not without dilithium crystals. We can't even generate enough power to fire our weapons.
...
SCOTT: Our shields will hold for a few passes, but without the matter-antimatter reactor, we've no chance. Captain, can you not call Starfleet on this emergency?
...
SPOCK: Captain, these are crude crystals. There is no way to judge what the unusual shapes will do to the energy flow.
...
SCOTT: Aye, that could blow us up just as effectively as...
Note: Scott specifies only ONE M/AM reactor but multiple antimatter pods. It is possible that the matter/antimatter reactor could contain multiple reactors (thus the multiple pods). Also with the dilithium sabotaged and no bypass available the m/am nacelles are unable to function indicating that they are dependent on some part of the energiser/dilithium machinery. Presumably the crystals need to be charged up.
I'll use that to segue into one of the apparent functions of the dilithium crystals in the series - they were super capacitors (or batteries) that also generated (or "regenerated") antimatter fuel:
"The Doomsday Machine" - 35
PALMER: Sir, Deck seven reports power failure in main energisers. Implementing emergency procedures. Severe casualties reported on decks three and four. Damage control party sealing off inner hull rupture.
SPOCK: It has ceased fire. We're being held in a tractor beam. We're being pulled inside, Commodore. You must veer off.
DECKER: Maintain phaser fire, helmsman.
SPOCK: We have lost warp power. If we don't break the tractor beam within sixty seconds, we never will.
Note: Warp power went when the main energisers failed and the dilithium crystals are tied to the energisers in "The Alternative Factor".
"The Alternative Factor" - 20
MASTERS: Whatever that phenomenon was, it drained almost all of our crystals completely. It could mean trouble.
KIRK: You have a talent for understatement, Lieutenant. Without full crystal power, our orbit will begin to decay in ten hours. Re-amplify immediately.
...
KIRK: Out of the question. Those crystals are the very heart of the power of my ship.
...
Captain's log, stardate 3088.7. We are no closer to finding an answer to the strange phenomenon than we were at the beginning. Not only have two of my crewmen been attacked, two of our dilithium crystals are missing, and without them the Enterprise cannot operate at full power. They must be found.
Note: Interestingly, not antimatter power exactly but "crystal power". This would suggest that the dilithium crystals on the Enterprise are like super capacitors or batteries that are charged up/amplified by presumably the matter/antimatter reactor. It is the dilithium energy that makes the warp propulsion go as well as generate fuel. The energisers not only provide power and fuel to the ship's systems but also act as a recharging mechanism as well. Full power means all four crystals (charged up) and/or the ability to create fuel (regenerate) at a specific rate.
LAZARUS: That's very bad, Captain. If he comes through at a time of his own choosing. But I think if we hurry and you will help me, he can yet still be stopped. There's little time left. He meant to come through. When you accidentally passed through, it drained his crystals. It'll take him about ten minutes to re-energise with the equipment aboard his ship. That should give us enough time.
Note: Lazarus uses the crystals also as a super capacitor.
SPOCK: Source of radiation, Captain.
KIRK: How is it the scanners didn't pick it up before?
SPOCK: Because it is not there.
KIRK: Another riddle? First Doctor McCoy, then you?
SPOCK: What I mean, Captain, is that according to our usual scanning procedures, there is nothing there that could be causing that effect.
KIRK: But it is there.
SPOCK: Affirmative. I confess I am somewhat at a loss for words. It may be described, though loosely and inaccurately, as a rip in our universe.
KIRK: A what?
SPOCK: A kind of physical warp, Captain, in which none of our established physical laws apply with any regularity. However, with the dilithium crystals, I was able to localise it.
LAZARUS: Yes! That's it! The dilithium crystals. With their power we could do it.
Note: Interestingly, with powered dilithium you can spot or create an opening from the antimatter universe. And when large amounts of antimatter come through from the antimatter universe the crystals are drained.
"The Paradise Syndrome" - 58
SPOCK: All engines stop. Hold position here.
SCOTT: All engines stop, sir.
SPOCK: Prepare to activate deflectors.
SULU: Aye, sir.
CHEKOV: Power dropping, sir.
SPOCK: Engineering, maintain full power. Full power.
SCOTT: Dilithium crystal circuit's failing, sir. We'll have to replace it.
Note: Scotty has ejected one of the crystals which explains why the ship isn't at full power.
SPOCK: Not now.
CHEKOV: Zero. Deflection point now, sir.
SPOCK: Activate deflectors.
CHEKOV: Power dropping, sir.
SPOCK: Degree of deflection, Mister Sulu.
SULU: Not enough, Mister Spock. It's only point zero zero one three degrees.
SPOCK: Recircuit power to engines. Maximum speed heading three seven mark zero one zero.
Note: This could go either way. The M/AM reactors in the engines at this point are sending power back to the energizers instead of creating a space warp for propulsion and now are recircuited to propulsion again. Or, the energizer is not sending power to the nacelles because they are going to the deflectors. However, the later Ep 77 "Day of the Dove" would suggest that there is M/AM in the nacelles and more than likely power was being routed down to the energizers.
"The Day of the Dove" - 66
SCOTT: The ship's dilithium crystals are deteriorating. We can't stop the process.
KIRK: Time factor?
SCOTT: In twelve minutes, we'll be totally without engine power.
...
SCOTT: There's no change, Captain. The dilithium crystals are discharging.
Note: Continuing evidence that the crystals store power even in a later episode.