I put the supers back on, usually above the inner cover, so the bees will pull the last trace of honey back down into the brood nest. During this time, the bees also protect the wax and I pull them off once we get some overnight freezing temps to knock the moths down. On rare occassion, the bees have moved up into the super and the queen begins laying in it. Thats an entirely different problem which then causes me to make frame manipulations to squeeze them back down into 2 boxes. If I was running 100's of colonys, my style would be different, but with only a couple dozen, I don't mind the time with the bees.