You could very easily know where the queen is. Slip a Q/E between the brood boxes and wait, at most, three days before checking again - all providing you can see eggs!
If in a rush, hope she is in the bottom and shake the bees from the shallow brood frames into the bottom box as you re-arrange them. The nurse bees will return to the upper box in a short time.
They may not raise queen cells, of course, and the process is far easier if using a second deep and demaree more properly.
Box of mostly foundation at the bottom with only one or two frames of brood and the queen and the rest of the brood up top of stack. The advantage here is that if no queen cells were drawn, or you wanted another cell you could swap fresh eggs and open brood to the top later. Putting the brooded frames upstairs and emerged frames back in the bottom will help to maintain a large foraging colony with maximum swarm avoidance. After three weeks you could be on double brood rather than a brood and a half, if you wished.
RAB