The good news is, the hive accepted the new queen and she quickly went to work... tons of brood, larvae and eggs in just a week! The bad news is, even though I put her in the bottom super with another large super above then a queen excluder with a medium super on top, she apparently started on top (where brood and larvae now are) and then went to the middle box which has tiny eggs.
So what do I do to have a box of honey with no brood if the queen excluder doesn't work?
This hive had a virgin (I assume) queen which I am almost positive I squashed when putting in the queen cage. When I saw her, I might have split the hive (again), but there were NO eggs, larvae or brood of any size. The new queen was marked, but when I saw her today, she wasn't. I'm assuming (though yes, I know what assuming does!) they just cleaned her off and she is the one I purchased since the laying activity has drastically changed this week. The hive has a much better temperment as well, since they are no longer in peril. Don't queen excluders normally work? She didn't look any smaller than any other queen to my somewhat inexperienced eyes anyway.