The main question after dealing with mites & going into winter, is how much honey is stored in each hive...?
Experienced beekeepers in your area can tell you the minimum honey stores recommended for a typical winter in your area - remember, all beekeeping is local. I would guess that a second super mostly filled with honey would probably be enough in NC, but you will need to check on honey stores in Feb and Mar. Be ready for emergency feeding at that time if necessary - that is a subject unto itself.
Early in the season, it is common to find the brood nest in a super above the hive body, it is a natural thing to see. As the honey flow develops, the upper frames are filled with honey pushing the brood nest back down to the lower hive body. In spring, I'd say don't worry about the brood nest in a super because the honey flow will push it back down. In fall, I would consolidate the brood nest in the bottom hive body, while placing honey frames on both sides of the brood nest and in the supers above it.
With the brood nest in a super, I'd give special attention to honey stores and making a plan for feeding over winter. I'd recommend you become an expert on emergency feeding in cold temperatures. That means planning to feed granular sugar, sugar boards, fondant and the like. HTH