It is hard to catch a time when the medium will be in a configuration that can be safely rotated with out disrupting the brood cluster. A good brood cluster will usually extend greater than the space in a medium. If that can be understood. sometime I have problems explaining simple things.
What I would do. I would get something to sit the boxes on. Take the top, medium super off, with the lid on.
Sit it on another bottom board, to keep from squashing any bees. Do the same with the bottom, deep box.
Now put a deep with foundation, starter strips, or drawn comb if you have it, or what ever you are using on the bottom board and put the two original boxes on in the order they came off. If your queen goes back down the bees will fill the medium with honey.
Now the question is, did the person you got the colonies from treat with that medium on? or did you after you got it?
If you could catch it after all the brood is capped, put a new honey super under it, but on top of the two deeps. After brood is capped it needs very little tending. Once the brood hatches remove the super and take out the old wax if you are not sure what chemicals has been used.
All this should give you plenty to do while you are waiting for other things to come into play. :)doak