sawdstmaker and deepcreek have it covered.
It is easy to move them to where you want them to be. However, to make the move you really need to consider the time of year and how many weeks you've got in your area for them to re-establish the nest in the new box and be able to fill it. They will need a month. If there is not enough time in your area, then do not move anything. Wait until spring - early summer and make the moves then.
If I understand correctly, you have the deep on the bottom and medium on top. And the bees are hanging out in the medium. Dead simple. Go into the hive. Physically pick up the queen. Place her on the top bar of a frame in the bottom box, deep. Once she has walked down, put a queen excluder on the deep then put the medium back on. Come back in 3 to 4 weeks; all brood will have emerged out of the medium and there will be a new full brood nest in the bottom deep. Simply remove the medium set it aside away from the bottom deep and remove the QE. Check through the bees in the medium. There is a slight risk that they have raised queen cells and virgins in the upper box. Once you are sure their is neither, shake all the bees from the medium onto the top bars of the bottom deep. Put the cover on and walk away. The medium may be full of honey. However they will have also filled the bottom deep below the excluder with what they and the queen need down there.
The queen excluder is a great tool for manipulating queens to be in the box(es) that you want them to be. Use it. Left to her own devices the queen will go wherever she darn well pleases - including right up the bottom of the top cover on a 5 story hive. There are certain norms or commons about where she will usually be and where the bees will put resources, but do not count on that. If you have a need for things to be a certain way for hive management, then use the tools that are available to do that.
Hope that helps!