Update.....
If you use Demaree as a swarm control method and want to raise a new queen from one of the swarm cells you can have the artificial swarm (original queen and flying bees) in the bottom brood box and all brood frames and selected queen cell in the top brood box above the suoers with its own entrance. To stop the new queen when mated from laying in supers, it is common to put a queen excluder over top super.
If you are not wanting to raise a new queen you cut out all queen cells in the top box (checking and cutting out any new ones after a few days). You don't need a top entrance or top queen excluder in this case.
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