Any frames in supers I’ve not extracted I put under the main 14x12 brood box. Leave on for just a few days for them to sort it out… you could always just store the supers over winter “wet” I.e uncleared by the bees. Then inspect the brood box, I’ll look for about 4 frames of stores, if not I’ll put a fondant on when I do my varroa treatment. Last year my Bees on 14x12 ate x2 full frames of food through winter, but your Bees will be different and eat differing amounts, but don’t worry about having to keep a super of honey on, more than enough space in the hive, just make sure they have filled enough stores frames.