First year ever having bees…Ok, so our bottom box is in excellent shape. All the combs are straight and filled out with lots of brood and honey. We added a second box wanting the bees to fill with honey for their winter feed. It took them over a month to move up and we checked on them regularly with nothing happening. Then we let it go for 3 weeks and checked and they have made a ton of honey but they built it all cross comb through six frames!! So do I mess with it and ruin some of their winter food or leave it and they can have through the winter and next spring it would be easier to straighten up because the honey would be gone??
I would leave it and if it appears full give them another box
I agree with @Bubba, If you go with foundationless frames you really need to keep an eye on the comb being built, it is so easy to get caught out as you have had happen. If you still have a flow happening you could add another box for winter stores.
Welcome to the forum, lots to read and friendly people to give you good advise.
Regards
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Thank you for your help! Do you also remove the queen excluder in the winter?
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Definitely. 
Don’t really even know why you have one on if you are down to two boxes. Is it above the lowest brood box? Wherever it is, it needs to come off, or you risk freezing the queen in your climate if the cluster moves above it.