Ive never worked with an inner cover (we dont use them here in FL) so I cant speak to that method. A few questions; are you sure you have a queen? have you checked to see how clogged and bound the bottom deep is? If the bottom deep is also bound with honey you need to create some space for her to lay, putting the excluder on just forced her to stay in that bottom box, why not remove the excluder and see if she will move up to the super. I would put the excluder under the deep full of honey so they continue to filll and cap it. Its all about space they will continue to swarm, and eventually die without proper space to lay brood. The second hive sounds like you may have a failing queen, no queen, or laying workers. That sounds like a lot of drone brood for 1 chamber. Look for eggs and a queen, they are backfilling it for a reason, usually a queen that cant/wont keep the pace or no queen at all.