They will naturally start backfilling from the top box and force the queen back down into the lower boxes. You don't need to do anything.
You could always manually place the queen back down below any box you want (with queen excluder), but make sure you do this after any chance of cold night temps have passed.
I'd just wait till they back fill the first top box, probably at the beginning of the flow, then slap a few extra supers on top.