That helps Stephen, thanks. The empty super is why they built loads of wild comb. If there is more than a beespace anywhere then bees will fill it with comb. A lesson well learnt. You need to do a couple of things now. Go through your bees gently and calmly four days after you wen through them last time. First of all go through the super that is on top of the queen excluder. Dont look for the queen but look for eggs. If you find any then you know the queen is up there. You have two choices, if you want to give the bees more room then put that super UNDER your brood box and put a fresh super ontop of the queen excluder. Or, if you do not want the faff of brood and a half then find the queen and pop her in the brood box under the queen excluder. If there are no eggs then take off the super and check the brood box again looking for eggs but keeping an eye open for emergency queen cells. If there are eggs then you have the queen in the brood box and all is OK. If you cant find eggs anywhere then you need to remove all but two of the queen cells. It means you have most likely lost your queen. I think the latter scenario is highly unlikely so dont despair.
Look at the blog page on this site and put my avatar name in the filter. There are some pages on there that will give you hints about looking after your bees as a newbee. Take heart, all is not lost and the bees will do everything they can to rectify your mistakes
Let us know how it goes