mslinn; are you running the appropriate aticonfig command after install ? Going from memory, but I think it would be something like :
sudo aticonfig --initial=dual-head --adapter=all
If you run aticonfig --help and look at the end of the resulting output you'll find details on these options. Further up are options to let you control where the screens are placed.
You *might* also want to disable RandR support if you're using multiple cards -- not sure if that is still required or if we figured out how to make RandR (which is still single-card oriented) coexist with multicard support -- but make sure you're running the right setup commands first and let us know what happens.
Hopefully xrandr will add multi-head and multi-card support so that it can fix things like that
Yeah... the hard part is that the RandR model assumes all displays are in the same frame buffer, which simplifies the rest of the graphics stack.
Going to multi-card means that drawing commands all need to be checked against card boundaries and executed on one or both GPUs depending on whether the window (and the operation) cross the line between cards.