Parts of the way Aperture (3.2.4 on SL) uses screens seems to depend on what mode you are in, (browers, viewer, combined) what mode you are in when you went full screen, what the setting for Secondary display is, and I suspect other things previously thought only to affect the flavour of pizza.
I have had two situations that I wanted to use 3 screens:
Scenario 1. I want to use two screens to run aperture, and one to run keynote. Can’t do that unless I keep keynote on top of an aperture screen.
Scenario 2. I want a browser on screen 1, my keyword HUD and my metadata inspector on screen 2 and my expanded selections on screen 3.