I've spent the last weeks drafting deck plans for the engineering hull that as much as possible accurately accomodate all the sets and corridors we've seen in the series and include a feasible turbolift system. I started below at engineering deck 14 and almost literally worked my way up to arrive today on deck 8 - where I placed the Auxilary Control Room in the bow. So I apologize being late to this discussion.
The way I see it, the information from "I, Mudd", that Auxilary Control is on deck 8, has led to the widespread assumption it's on deck 8 in the saucer hull (although there is no such hint in The Making of ST
However, as I suggested in another discussion, some decks on the ship are identified by their function with an alphabetic letter:
"H deck" ("Naked Time") is hangar deck or engineering deck 13,
"B deck" ("Court Martial") is berth deck or main deck 6 etc.
If main deck 8 would actually be the "R(ecreation) Deck", there'd be no need in the ship's lingo to refer to "engineering deck 8" as every man and woman aboard would understand "deck 8" to be engineering deck 8 as main deck 8 is R deck.
If main deck 2 would actually be the Quarterdeck or Q deck, then "deck 2" ("Enterprise Incident") would instantly become engineering deck 2.
As we've seen in the series, there are two locations in the saucer from where the ship can be controlled: The Bridge and the "Engine Control Room" ("Naked Time", "Space Seed"). I think yet another location to be rather redundant.
As for the operation of the engineering hull or star-drive section without the saucer - as suggested by The Making of ST
-the engineering hull should obviously have some kind of bridge and that's where Auxilary Control comes in (and if it's on engineering deck 8, then Scotty's ladder descent to the "Engineering Section" of the Constellation
makes perfect sense in "Doomsday Machine", IMHO).
And then, there's of course the "Emergency Manual Monitor" on the upper level of the engineering section from Season Two onwards.
The one thing I'm trying to make sense of is the location of "Life Support" in "By Any Other Name". It appears to be the same set as Auxilary Control. I think this one should be on the same deck as the Herbarium, probably (main) deck 8.