On a nice warm sunny day. Put all your bee protective gear on. Do not use any smoke. You purposely want them all flipped out and as flighty as possible so they will readily go back to their hive entrance. Take the extra box(es) off. Make sure the queen is in the bottom box. Proceed to shake out the bees on the ground directly in front of the entrance of the respective hive. Put the box(es) in a sunny spot at the farthest end of the yard away from the hives. Tip up on end so frames are vertical, set the boxes next to each other, stack like a pyramid. Tell everyone to stay out of the yard for at least 3 hours afterwards. Leave the boxes out there for 2 to 4 days while the bees to rob them out and take the honey back to the hive. It is going to get BeeZee around those boxes so make sure they are not in a people traffic area. If there is brood in them, too bad, lost at this point. That is the fastest way of doing it. 2 to 3 days of nice weather and the boxes will be bone dry. Note allowing robbing is illegal in some jurisdictions and is also typically discouraged if not illegal by town bylaws. Ensure your neighbours do not notice your bees and if they do, ensure you know the applicable regulations and bylaws beforehand.
An alternate, much slower but less beeziness in the airways way of doing it is. Removed the extra boxes. Shake out as described. Put a queen excluder on top of the bottom box. Put an inner cover with open centre hole on top of the queen excluder. Put the extra box on top of the inner cover. Put the lid on. The bees will go up and recognizing the combs are separated from their nest, they will move as much of it as they can down into the brood nest. This method will take 1 to 2 weeks for them to pull the honey down below, and no guarantees they will. They may just keep using it up there as storage.
Some ideas for you.