I really think the current shipyard area should be scrapped and moved to operations.
Have Kurdland in his office and such.
And I really think the Observation Deck is way underused, the current exchange and mail area could be moved up there.
Next the hallways in quarks are way to freaking big, i'd say just get rid of them and put in turbolifts.
Next make Quarks bar part of the main zone, make it accessible from observation deck like in the show, also make the doors open an close that lead to the prom, and open up the bar area on that has seating on the prom.
Next get ride of the cargo bays were the exchange the and the shipyard were.
Move the medical officer near the infirmary for now, at least until you open the infirmary up.