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?