Well we do know that Engineering has many decks.
"Where No Man Has Gone Before"
CREWMAN: Engineering deck three, can you give damage report?
"The Conscience of the King"
KIRK: Lieutenant Kevin Riley in communications, I wish to have him transferred down to the engineering decks.
"The Corbomite Maneuver"
KIRK: Helmsman, engineering decks could have been faster, too.
"The Enemy Within"
KIRK: The lower levels. The Engineering deck.
SCOTT: Mister Scott, sir, on the lower level of the Engineering deck.
And there are references to decks in general by number such as "Deck 12", "Deck 14", "Deck 8" and also "H Deck", "B Deck".
In my personal view, I think there are probably multiple deck schemes going on.
- A named deck, such as "Engineering Deck" can contain multiple levels. There are also multiple "Engineering Decks", most likely because of the Engineering section.
- Decks 1-20 (or more) are probably all decks, top to bottom. In my version of the Enterprise, Deck 10 is the neck area. Deck 11 is the top of the Engineering section for me. This is partly due to how many decks I can fit in on the Primary hull.
- Alpha letter decks are probably primary hull decks - since "B Deck" seems to be a good place to sabotage impulse engines while in orbit in "Court Martial".
Anyway, that's just my thinking and YMMV