Counting up from the bottom, relative to--something?
As late as "Day of the Dove", it seems that some writers counted from bottom to top. Kirk and pals hold the bridge of the ship, and supposedly the other top decks as well - "All sections above". Klingons in turn are said to be holding Deck 6 and half of Deck 7 - and it would make rather limited sense for the Klingons and the heroes to be contesting a deck that's below
a totally Klingon-controlled deck!
However, 90% of the crew were sealed off "below decks" as well. If the Klingons occupied the lower parts of the ship and Kirk's gang all levels above, where on earth were the missing crew?
Good question. If we assume Deck 1 was top then:
KIRK: What the blazes is going on?
SPOCK: Scans indicate that our forces and those of the Klingons are exactly equal at thirty eight each. The Klingons control deck six and starboard deck seven, while we control all sections above.
could be interpreted that the uncontrolled decks below deck 7 (and port deck seven) contain trapped Enterprise crewmembers.
Now, if Deck 6 and parts of Deck 7 are the lower parts of the saucer then that would indicate uncontrolled passages going down the neck to the engineering hull and that would be where the main fighting is occurring for strategic control of the ship, IMHO. Also, it's pretty easy to have 390+ crewmen trapped below deck 7 spread across 12-13 decks.
The final fight in the engineering hull would indicate that both sides could get to the engine room uncontested.