I currently run Ubuntu 11.10 with Unity and FGLRX driver. I also use two monitors. Right now, if I maximize a window it does so across both screens. In addition, things like alt-tab will display split across both screens. It seems as if the computer is running with one giant desktop as opposed to two seperate desktops (workspaces?) as it did with the open source driver.
And no, I cannot go back to the open source drivers as they do not support hybrid graphics like the FGLRX drivers do.