I am very new to beekeeping. I have 8 frame hive boxes. When I got the package of bees I followed the instructions to leave a frame out to let the queen box hang. When I checked on them a few weeks later they had attached comb to the inside box and not knowing any better I left it and added another box. I just slid it in place and left another frame out. So now I have a mess. I tried to take the cover off the other day and the bees were not happy with me. I’m not sure what to do. Please help. I try love my little friends and I want to fix this the right way. Thanks
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Hi Elizabeth and welcome! Congrats on your new box of messy friends 
Can you post some pics to give us an idea of how bad it is?
Cross combing and bridge combing can be cleaned up using your hive tool and a bread knife, with a serving tray or large bowl handy to drop the comb chunks on/in as you work. If your frames are cross combed, you’ll have to carefully cut sections out of the frames after separating them with the knife, and rubber band them back in place. Best to use a tray for this, and place the sections gently down on it, trying not to pin bees underneath. This is best done with a helper who can hold the frame for you while you stretch about 4-5 big rubber bands on vertically, and slot all the salvageable pieces of comb back in alignment with the frame. Bridge and burr comb are much less disruptive to clean up, just scrape along the hive parts wherever comb should not be, going slowly and nudging any bees out of your way with your other hand. You might get lucky and have an early taste of honey if the bees have begun storing it in this comb! You can save the wax in the freezer - it adds up to a votive candle in no time, and you’ll need it to prime your Flow frames if you have them.
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Welcome to the forum Elizabeth, lots to read and bee keepers here happy to pass on advice and tips.
With an 8 frame brood box there is enough room for 8 frames and to snug the queen cage in between two of the frames.
I don’t know why you were advised to leave a frame out. With a 10 frame brood box there isn’t enough sideways movement to fit the queen cage in but that isn’t a problem with an 8 frame box.
Cross combing and bridging comb will happen if the frames are not sitting shoulder to shoulder and will happen more often with foundationless frames. The queen should have been released from the cage in 3 or 4 days by the bees and the cage removed then.
The job now is to tidy up the frames so that there in no comb outside the frames and using rubber bands as Eva says is an option to hold everything in place. Put the eighth frame into the box. The sooner you do it the better, once bees start making wonky comb you need to interfere or it will continue.
Do it slow and smooth, use smoke, the bees will be angry but they don’t know your trying to help them.
Cheers
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Seeing comb being built in the roof is something of a warning sign that the colony needs more space to expand. If the hive is really packed with bees and the frames have 80% plus of the frames in use with brood, nectar, honey and pollen then I would either add another brood box or add the super with a QX depending on your climate. Check with local bee keepers if a double brood hives is in use there. Scrape the comb off that is in the roof. Using a hive mat is a good step in reducing comb being built in the roof, it acts like a mental barrier and so the bees don’t tend to make comb above it even thou the bees can go over the mat.
If you have larvae in the brood then you have a laying queen doing her thing, and that is all you need to see, it is nice to see a queen but they are shy and tend to hide out of the sun light.
Cheers