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If you do use a queen excluder and place the empty super on top, the bees can be very reluctant to move up into the honey super. They almost need a reason to squeeze through the excluder to go into the empty super. Since you have to deeps I would place all of the brood and queen in the bottom deep, next the queen excluder, next your honey super then the other deep with honey in it. If you leave brood in the upper deep they may try making a queen cell in it.