Doing a search against use of "levels" in TOS it would appear that the Engineering deck possesses multiple levels. Levels do not appear to be referred to on other decks so it might be safe to say in "The Naked Time" and "Omega Glory" that "level two" and "lower levels" were understood to be on the "Engineering deck". Interestingly, then if the engineering deck starts at the Engine Room there would be a maze of "levels" at the top (think EMM) going into the bowels of the engineering hull... The Enemy Within: SCOTT [OC]: Mister Scott, sir, on the lower level of the Engineering deck. The Ultimate Computer: SPOCK: There is one possibility. The automatic helm navigation circuit relays might be disrupted from engineering level three. The Naked Time: UHURA: Sir, level two, corridor three reports a disturbance. Mister Sulu chasing crewmen with a sword. The Omega Glory: SPOCK: Lieutenant Galloway and I are checking out the lower levels. There seems to be no one aboard. Only uniforms. The Man Trap: SPOCK: Supplies of salt have been set out as bait at all decks and engineering levels, Captain. However, no one or nothing has approached them as yet.
The "Man Trap" reference especially would seem to make the "levels are parts of an Engineering maze" interpretation vastly preferable. If it's anything like the STXI facility beyond those neat and tidy control rooms, then a "level" is probably very different from a "deck", and in practice represents an odd "fraction of deck". The one canon view into the TOS engineering spaces, the Drexler diagram from a parallel universe, indeed suggests loss of deck structure coherence when one moves down to the Engineering Hull. It's probably restored in the after parts of that hull, though, making it particularly valid to label one of the decks "Hangar Deck" specifically: little else but the hangar is to be found on that deck, if the corresponding forward hull spaces are but a jumble of catwalks. The one thing we probably don't need to bother with is attempting to keep curved corridors away from the secondary hull when assigning identities to named and numbered decks. We have to accept that the sets "lie" to some degree in any case, as the ship just plain cannot have circular corridors of the exact same curvature or radius; sometimes the set has to be interpreted as having shallower curves than it actually does, sometimes sharper ones. The Engineering Hull might feature lots of "shallow S" corridors snaking past bulky pieces of machinery, say. Shallow curving might also be necessary in the problematic hull support pylon: a straight corridor running down the middle would divide the space into uselessly small halves, but a corridor curving along one side would leave maximally useful rooms on the other. Not that too many decks in the neck would have corridors - but Deck 12 just might. Timo Saloniemi
Traditionally, in Navy ships, decks run the length of a hull, flats or platforms are partial "decks" and levels are superstructure "decks." IIRC, deck numbering begins with the main deck/weather deck as deck 1 and numbers increase as you approach the keel. IOW, Deck 2 is below Deck 1. The level above the main deck was Level 01 and numbers increased toward the masthead. On the ship I was stationed on, our bridge was on Level 05. Which often makes me ponder, what if our a priori Bridge = Deck 1 is wrong?
Just a guess, but would "super-structure" (lat.above structure) not simply refer to "decks" above the weather deck? As per the example (Level 01 etc). There's just no room (or point) in having 8' wide corridors in the neck pylon - the neck is only 16' at it's widest, even before allowance for hull thickness is taken into account. The corridor (S-shaped or not) would obscure most of the floorspace - might as well widen it to accomodate the whole deck!
The floors in the built-up structure above the hull. "Levels are 'decks' in the superstructure" would have been better way to say it. This illustrates the concept although level isn't labeled: http://www.princeton.edu/~abraitis/pics/decks.gif