Everyone knows that engineering is "downstairs," somewhere in the secondary hull, right?
Looks like I missed this thread.
Apparently the star drive engineering section is in the engineering hull and the location the alien entity exits the ship in "Day of the Dove" can be taken as sufficient evidence.
However, the Season One set blueprints clearly reveal that the "Engineering Control Room" ("The Naked Time") is obviously on the port side of the saucer (leaving enough space in the center for a turboshaft).
In addition the context of "Court-Martial" is pretty clear about Finney having sabotaged the Impulse engines and that he is somewhere on the impulse deck ("B Deck" = "Berth Deck" = Main Deck 6, IMHO).