Well I continue to learn and I will certainly learn after today. I had two problems which I tried to solve simultaneously - we'll see.
First, to go back, it looks like the swarm I captured may, in fact, have been from my hive #1. As I have noted before, they have been reticent to move up to a new box and got brood bound - in other words they had no place to lay their brood, therefore they had to swarm to continue to reproduce. So swarm they did.
As a result I have been thinking about how to break up the brood area. One method is called checker boarding - this is when you make room in the brood nest by taking out some of the frames of brood and replacing them with empty foundation or comb, this gives the bees something to do instead of swarm. Usually you would take the removed frames and put them in a box on top of the brood box and thereby expand the brood into the upper box. However, in the set-up that I had the upper box was a "medium", and the bottom box was a "deep", ie they were different sizes, therefore I could not move the frames from the bottom to the top box - they would not fit :(
Problem #2 - Hive #2 was from the first captured swarm but was also originally on a deep. However, this deep had a mixture of deep and medium frames (the medium frames will fit in a deep but the deep frames will not fit in a medium). These bees had already pulled and populated a full medium with brood, pollen and honey on top of this deep.
SOoo, what I did today was take the deep box from the bottom of hive #2 to the top of hive #1 thereby making the brood nest for hive #1 two deep boxes. I only transferred over the deep frames and brushed all of the bees off first. I also did some checker boarding with the bottom box so hopefully the bees will have plenty of room to expand the brood.
Then, I took the full brood box(medium) from the top of hive #2 and made it the new bottom of hive #2. I added the partially drawn medium that was on the very top of hive #2 and the medium frames from the deep that was the bottom of hive #2 and this became the top brood box of hive #2. Now in doing all of this I tried not to confuse the bees. I brushed all of the bees into their respective hives regardless of what frames they came from. There will be bees that emerge from brood cells that came from the other hive, but I am hoping they will adopt them.
My real worry is the queens. I looked as I was going (but I did not want to take the time to look real hard) but I did not see them. As I said, I brushed or shook all of the bees into their respective hives, so I am hoping that they are where they belong.
Honestly, I have no idea what confusion I have caused. Either I did a really good thing or a really stupid thing - we'll see...
Here is a picture of the hives in their new configuration. Hive #1 is on the right and hive #2 is on the left.
Here by the way is hive #3 - the captured swarm - they have been building like crazy - but I have yet to see any brood. Aargh, I still don't get these bees! :)