If you have two deep brood boxes full the bees will winter nicely in them and it is good to take the supers off. Set the supers off and unless the hive bodies feel light when you lift the hive, you are fine for the winter. The capped super can be extracted and since you seem to still have some honey coming in if the bees are drawing on the partial box, they may very well fill the extracted box again. If you don't remove the supers, the bees will be raising brood in them come spring. If the queen excluder is still on, the bees may abandon the queen if they move up past the excluder for the stores. If you have had a queen excluder over your hive bodies, the bees would not have filled supers if there was still room below! So extract your honey and take the supers off when the bees stop bringing in honey. Extract again if there is enough.