OK, so the reason I couldn't find the queen, and there was no brood of any kind in the brood chamber? Yep, queen trapped above the excluder, one honey super full of brood. I figure she dropped down onto one with the opened hive stacked last time.

(For MB, all you "honey excluder" and continuous broodnest people... all together, with feeling: "I told you so". Thanks )

Anyway here's my newbie quandry. I'm requeening next week, so I was in the hive today to check stores and to cage up the queen (both to break the brood cycle, and so I can pop her out in the evening easily and introduce the new lady in the morning). I caged her in the lower deep, what used to be the brood box. I left out the excluder (what's the use with the queen caged), and left the broody honey super just over the stores deep. See diagram (you may have to expand the window th read the labels):
http://www.totalupload.com/uploads/c5f1833531.jpg

Need I put the brood closer to the (caged) queen? I'd like to not leave that shallow on for the winter, so if they'll hatch out the brood to later join the new (laying) queen below but still keep the queen alive for a week, I'd just as soon use this setup and go into winter with just the two deeps. There's a good population of bees; I think they could fill both areas adequately. It's hot daytimes here, 50s at night.

Good plan or fool's errand?

<edit> And also, I should start feeding now, a week in advance of introduction, right? That's why there's a deep on top of the Tarheit-inspired ventilation box, for a gallon mason jar.