The wings would contain inorganic stores, the landers, and the business part of the FTL drive. The rings forge the warp, and the wings accelerate it. When the warp is in place, the wings are uninhabitable.
The landers have legs that fold out from the "heat shield".
As for the lower decks, you are right about the inefficiencies. But the layout is governed by the way the ship creates gravity. It accelerates in real space at one gee, and the acceleration creates an artificial gravity pushing against the direction of motion. If you reversed the decks, the people would be walking on the ceiling.