Are you running "brood and a half"? (Its better thansingle brood for overwintering ... but then I like 14x12, which is like brood and a half but with single deeper frames.)
Simplest way to get to brood and a half would be to put the brood box with foundation on the hive floor and rearrange your shallow frames to have the best 11 (most brood) in one box and put it on top of the deep box.
And I'd put a feeder on top of the lot with 50/50 syrup (equal weights of sugar and water). Wax-making uses lots of fuel - make sure they don't go short!
Bees naturally draw comb downwards, the wax-makers can then be in touch with the nurse bees, rather than being expected to go to work 8" or more away (if you put the big empty box on top). Wax-making below brood helps the bees (heat from wax-making rises into the brood), whereas in a box above, brood heat is being 'lost' into an empty box where wax-makers nevertheless would need to get themselves toasty warm to do their work ...
If you have one or two shallow frames with brood left over, I'd put them into the deep box, in place of foundation frames. Put them between deep frames, not next to one another, and I'd put them towards the outside (with a view to getting them out soon). Yes the bees will draw some wax beneath, but don't worry about it. Brood (future beepower) is what the colony needs to maximise right now. Boosted with more young bees, the colony can grow quickly, and will have the beepower to do the needful, including drawing out their deep box.
Any frames with zero brood (do check for eggs!) that have useful amounts of nectar/honey stores might be added to one of your other colonies.