Keyclone comes with some window layouts. While I have not tried doing a full screen on top of a full screen you can just alt-tab to do that in theory though if they are windows screens that just happen to fill up your desktop they will likely work faster.

Keyclone can also swap pips around as need be, just bind the keys to them.

I will say however, two screens == awesomeness. One for your main and one for your slave(s) is a very nice way to roll.