Don't beat yourself up about it. There isn't an experienced beekeeper alive that hasn't made some monumental mistakes. It's part of the learning process. They are amazingly complex creatures and you are doing your best to save them and I really applaud you for giving this a go, because many beekeepers wouldn't know where to start.
If you have taken the empty box out and they are starting to take more pollen in now, then I would hang fire on doing anything drastic and let the bees try to work it out. the fact that they have secured some of the comb into the frames and they are gathering pollen is all positive. Just spending time watching and listening to the activity at the entrance is both therapeutic and informative, although it takes time to read and understand what you see. There is a good book called "At the Hive Entrance" by Jorgen Tauzt (not sure if I've spelt that correctly) that might be helpful. I try to spend at least 5 mins every day when the bees are active and I'm pretty sure it helps the bees to get to know you too.
If you can, it would be beneficial to do the next cut out, with the improved knowledge you now have about keeping the combs the right way up and then, hopefully, you will have two colonies that can possibly be used to help each other or if necessary, united to make one strong colony, if one of them does end up queenless.
Don't be too keen to go out and buy a new queen. They are mass produced and mostly artificially inseminated and of coure unrelated to the bees that you have, Those are 3 good reasons why a queen raised by your own bees is better, in my opinion. To me, it is important to see the colony as a whole entity, rather than a collection of parts ( a queen, workers, drones, comb, honey) that can be interchanged or replaced at will by the beekeeper.
Just thinking about things as I type and if I were you, I would put a third deep box with frames and foundation on the bottom below the other two boxes, then the bees can build down into it when they are ready and hopefully that will allow them to make a new and better broodnest instead of trying to work with those mixed up combs. Eventually you should be able to harvest those combs out, if you keep putting an empty box below them as that comb will become filled with honey.
Hope that makes sense but if not ask.
Good luck and don't worry, bees can be amazingly resourceful of we let them,.