Thanks! I'm finally almost done with it!
I actually started out this way figuring that the coordinates of the monitor would stay fixed regardless of the other monitor's rotation, but BB doesn't like displaying a marquee unless the marquee monitor is to the right (it doesn't like the top, either. Bottom would probably work, too). Another post on the forum pointed out that they need to be the same DPI as well, which caught me at first.
I already have to wrap the emulators to handle screen rotation, so maybe I can just reposition the bigbox marquee display, too...