Re: Messy Foundationless Hive
What size and how many boxes are there in your hive? If 2 deeps, then you could wait until spring when both boxes are fairly full of bees, split the two boxes apart and put a super on top of each. There will most likely be eggs and young larva in both boxes so the box without the queen will make themselves another. After the split, when bees are again in two boxes, go thru and find the queens and put them in the upper boxes that have good comb, put those boxes on the bottom of the hive stacks with a queen excluder over it and then put the wild comb boxes on top. As brood emerges from the top wild boxes, they will fill the combs with honey. Once they are capped, you can then remove the wild comb boxes and crush and strain the honey out.
Whatever you decide to do, best of luck to you!
20+ years, raise my own queens, feed when needed, I treat but have not perfected varroa management yet.