rotate the boxes, however, move two or three frames of brood to the empty brood box to encourage the bees.
More than likely the empty brood box is empty cause the bees all hatched, and since the queen left the building many days ago, you now have an empty box.
Your small swarm is probably an after swarm. You probably lost the big one!
If you do not take care of those swarm cells, you will probably have more after swarms. I would leave only one cell...be carefull not to damage it...also GENTLY check the swarm cell you are keeping. very carefully check the bottom. Some time the cap is still on, but the queen vacated.
If the end of the swarm cell looks chewed...like a can opener opening a can, she is out. I have had cells where the queen left a small end not chewed, the "lid" closed over after she left.
Queen excluders work if used with some ingenuity. Place one frame of capped brood above the excluder to encourage the bees to move through it...make sure the queen stays in the bottom. And, if your frames are not drawn, spray with some sugar water to encourage the bees.
With the excluder, you can also turn it 90*. Normally but not 100% it will keep the queen in her place...not always... but it will give the bees space to move between the brood chamber and the honey super
You really do not want the queen laying in the honey supers...
1. as she lays in the super, the comb darkens and will darken you honey.
2. brood equalls pollen, your honey super will have pollen in it. Again darkening the comb.
3. honey supers with no brood in it has less of a chance with small hive beetles. If you are in an area with small hive beetles, they will damage your honey supers
4. If there is brood in a honey super, it is harder to remove the bees when you want to pull honey because they will want to stay with the brood. In essence a headache.
5. and this is a big one...If you manage your hives right, there is absolutely no reason why the queen should need the space to lay eggs in a honey super. It means that the brood chamber is to packed with honey. Get that hoeny out of the chamber and into the super.
Lastly, bees consume most of the syrup you give them in the spring. Rarely is there syrup in the brood chamber if you do it and time it right. More than likely, what you see is nectar that has not been dried and capped. It will run when not dried an capped
Best of luck