Mike R., sounds like what you had was a mess
. First off, bees don't make queens from brood. They only make queens from very young larva. They also won't make a new queen if they are happy with the one they have and aren't in a swarming mood. I would continue to try to get them all onto frames so you can learn and work with them. Take the comb and rubber band it into empty frames and let them tie the comb to the frames. I wouldn't have the super with just foundation in it next. I'd have the one with the brood, honey and foundation next. When that foundation is built out and covered with bee's, then add the box with just foundation.