Bill,
 
   Brood in the supers means the queen was there...  To stop this, either use a queen excluder
below the supers (...making sure the queen is below...) and/or make sure your bottom super
or top hive body is full of honey.  (The queen won't cross honey to lay above it.)
 
   Putting an excluder on now will trap any emerging drones up there, but they can be given a
top exit with a small rock under the top cover.  It's a bit like closing the barn door after the
horse is gone, as prevention sure is better than the cure on this one.  Note:  if you move the
super with brood very far above honey supers, the nurse bees up there will think they are
queenless and might start supersedure cells.  Watch for them.
 
   Have fun!