Well, here's an update. This afternoon was sunny and warm, so I went ahead with the second half of the inspection (bottom box, this one is a deep, whereas the two on top are mediums).
In the deep box the queen is laying a solid pattern on two frames. There's one half-drawn frame next to the brood, on the outside. On the far side of the brood, every frame has nectar and pollen in it. I still can't seem to find that dang queen, though. She's hiding somewhere. But the evidence of her existence is all over the frames, so I'm not too worried.
That said -- are 5 frames (2 deep, 3 medium) sufficient for her purposes? 6 if they finish drawing the one outside frame? If not, what should I do about it? There is one deep frame that has a good number of empty cells (no nectar or pollen) that I could move next to the brood nest if necessary. Otherwise, maybe I could shuffle the top around a bit to give her some room, then flip the top and bottom brood boxes. Any thoughts?