I think I keep making a problem bigger

It sounds like when you placed the queen excluder, you have kept the queen above the queen excluder and she kept on laying. At the same time, the bees bellow the queen excluder, the bees "thought" they are queen less and decided to make themselves a new queen. It might not be a swarm cell you saw, but a supersedure cell in the bottom box. Sometimes when bees lose close contact with their queen, if they have the resources, they will make a new queen.

So, not to worry...you can do different things with the situation you have created.

The good news is, your hive still has a laying queen. Hive has brood and its growing. Great.
If you do not want to make an increase at this time of the year, just destroy the queen cell below the excluder, remove the excluder, and let the bees settle with the new arrangement. While you are at it, look for other queen cells in there. If indeed they try to swarm, there will be way more that one queen cell...if they try to supersede, there will be just a few...it could be only one.

If you want to maintain the queen excluder in place, shake all the bess into the box bellow the excluder, put the excluder back and let the bees sort it out. By shaking all the bees, frame by frame into the lower box, most likely you will shake the queen also, without making the effort to locate her. Just make sure you remove the "swarm cell" you found.

If the box above the excluder is full of brood, and it should be, since the queen was there laying it up, you could reverse the boxes so that the one full of brood goes on the bottom, remove the queen excluder and place the bottom box in which you found the "swarm cell" above the box that has all the brood now. Just make sure you remove/destroy the queen cell. In this arrangement, the original queen can move up and continue laying in the box that should have plenty of room by now.

As for placing a modified QE in the entrance to prevent absconding...why? Why would you think your hive is trying to abscond?
Might want to look up the meaning of absconding, swarming and supersedure processes. Each one is initiated for different purposes...each one has a different dynamic...a different outcome.
We need to learn to understand them...especially if we do decide to intervene and have some degree of control over the outcome.

Good luck!

I don't want to sound like a know it all here Nate, and don't mean to be offensive at all just want to get a couple things cleared up and it will help you later on down the line.

1. Swarm/Supercedure/Emergency queen cells can actually be anywhere on the frames. You have to look at the situation under which the cells were built, how they were built and how many were built. I know that's a bit to keep track of but it gets easier as you go.

Based upon what you have said within your original post, i'm pretty sure what you got was either an Emergency Cell or Supercedure Cell. Which is just fine in any case.

Here's the break down of why I see it as an Emergency or Supercedure Cell. A. Queen Excluder with brood above and queen below. B. Only 1 Cell normally means Supersedure - Can also be Emergency if that was the only viable queenable larva/egg available. C. With the abscense of queen pharamones above the excluder it would put the young brood into a feeling of queenlessness causing them to want to make a queen under the emergency response.

Now to answer the question about using this cell in another hive. If i were in your shoes i WOULDN'T use this cell in another hive that you've tried getting them to raise a queen and have not done so. That in itself usually means there is a virgin in the hive or a mated queen that has not started laying. In either case you put a queen cell into that hive and the bees will either tear it down, or if she actually gets to emerge and you do have a queen in that hive that just hasn't started laying, she will get killed by the new virgin and doing so would just put you back further.

What I would do is as i stated to begin with. Then once she is mated up and laying if the other hive still hasn't started brooding up, do a combine at that time through a queen excluder. Shake out the bees from the bad hive through a queen excluder and you will find the one that is the DUD..

I hope this helps you out some..

OK guys thanks for the help. There are a few things I have to clear up. The queen-less hive I have; is a hive I got called out to do a cutout on and have had for 2 weeks with no signs of brood other than the brood I put in there from cutout and the frame I put in there to see if they would build queen cell, but plus side is no laying worker as of yet neither. Also, I understand the reason for absconding, swarming. The swarm cell or what I presume was a swarm cell was above queen excluder and the super was honey bound with no place to lay it was full. I believe they build a swarm cell cause of this. The reason my friend uses QE in entrance of a new hive is tehe hive is empty has no investment from bees so easy to leave. He put the excluder on and bees build for a few weeks queen is laying never saw one leave yet, since we started doing this, lost 2 before we did this. Maybe just luck don't know. I just did not know since I screwed up by getting queen above QE and they built swarm cell and it is this late in year if a person could redirect them by keeping both queens in hive which is dangerous outcome also cause drones cant leave neither.