Placing the bottoms on top, just means if they do not fill them, that a huge void area free from stores, will cause disaster in the winter. And any benefits from trapped heat is lost. Bees starving usually eat their way to the top where the can conserve energy by being up against the inner cover. this location also makes it easier for feeding.
But having a deep box on top with empty comb, works against all this. I would of left the comb where it was, and fed them. the bees would then put it where they wanted, etc.
Bees naturally back fill from the top down. They will fill as the flow dictates. And if they only fill have way down the brood chamber, then that is OK. They will eat up through what they have.
And for those in my area, if you have light hives in the beginning of September, you will probably have light hives at the end of September. Do not think they will pack in 50-60 pounds of honey from goldenrod or aster. If they are light, feed them now! They have lots of brood to raise in the next several weeks, and much of what will be collected in the field will be used for brood rearing.