If I'm understanding correctly, you have a 2 box hive and the bottom box is empty drawn combs with 2 combs full of honey? The top box is combs of honey and brood mostly? If this is so, I'd rotate the boxes, switching them to put the queen on the bottom. If the combs in the then top box are not drawn out correctly, then scrap them back with your hive tool so the bees can rebuild them out more correctly for you. If I've missunderstood
what you have then please disregard this reply!