Back in the 70's, Franz Joseph put the engine room at the back of the saucer, saying the pipes were part of the impulse engines.
Which annoys me, because he missed the point of the "pipe cathedral" set component, which was tapered in real life but was meant to be a forced-perspective component representing something that stretched out considerably farther (like the similar effect in the TMP engine room). Instead, he took it literally and had it tapered exactly as it was on the soundstage. I prefer the placement in Doug Drexler's cutaway.
"Day of the Dove" explicitly states that the secondary hull is cut off, and it's humans vs. Klingons in the saucer.
No, it doesn't. Nobody in the episode says anything about "the saucer" or "the secondary hull." All they say is:
Captain, reports coming in from the lower decks. Emergency bulkheads have closed. Almost four hundred crewmen are trapped down there, sir.
A graphic in the same episode suggests that the accessible sections do include part of the secondary hull:
http://tos.trekcore.com/gallery/albums/3x07/dayofdove_156.jpg
And at the end of the episode, we are explicitly shown the evil pinwheel entity emerging from the secondary hull after it passes through the engine room wall.
Also, "The Enemy Within" established that engineering was in "the lower levels" of the ship.
MoST also says that the HQ for engineering is in the saucer and that the secondary hull was mostly machine-shops, fuel, food, water reclamation, and is a minimal-crew section of the ship.
It says more than that about the secondary hull. From pp. 190-1:
The secondary hull is often referred to as the engineering hull, as much of the facilities and activity in this area are devoted to that department.... Minimal crew quarters are located in this hull, used by duty engineers and by the star-drive crew when the saucer has detached and is operating separately.
That tells me that the intent was for most of the engineering activity to go on in the secondary hull, particularly the "star-drive," i.e. warp drive. When the saucer was separated, the warp-drive crew working down in the engineering hull would need temporary quarters during downtime. Its statement about headquarters and control facilities being in the saucer suggests an administrative/control area being separate from the actual lower workings of the engines themselves, which would've taken up most of the secondary hull.
However, TMoST, while useful, is of course superseded by canonical information. We saw that the standard engine room set was in "the lower levels" in "The Enemy Within," and we saw in "Elaan of Troyius" that the same room contains direct access to the dilithium crystals that channel warp power, which wouldn't make any sense if it were in the saucer. So either there are two duplicate engine rooms, each with the same "pipe cathedral" in back (which doesn't make much sense), or the engine room is in the lower levels, period.
Here's a good article about the placement of engineering:
http://www.trekplace.com/article07.html
It offers extensive evidence that the engine room is in the engineering hull near the warp engines, and very little evidence to the contrary.