It is normal for bees to make queen cups. If there is no larva or egg in the cup it means nothing. You can move some of the partially drown frames from the top down to the second if you want. I have a swarm in a deep that I put a med of foundation on. I was in the middle of a heavy flow, they drew it out and filled it with honey in 8 days. I put another med of foundation on top do the deep and put the honey on top. They drew it out in 7 days most full of honey with a few of the center with small patches of brood. I added another med super of foundation on top of the hive. I expect if the flow continues they will start to draw and fill it.
That being said. I would think you would have a flow in Michigan but someone local would need to confirm that. By feeding you are simulating a flow. They will have to put the nectar some where. I would open up the brood or center frames of the second box if it is full of syrup. Unless you see eggs or larva in the queen cell there is nothing to worry about. Do not forget sometimes a package will supersede the queen.