With the ATI Restricted Drivers comes a tool called aticonfig which makes it very easy to setup two monitors. The only little problem I've noticed is how the Mac Pro/Mac OS X and the ATI Restricted Drivers/UbuntuÂ count the DVI ports. They count them in opposite directions.
If you turn on your Mac Pro only one display will be on at first. That is the main screen if you want. Once Mac OS X is up it will show the login dialog on the same screen. The ATI Restricted Drivers/Ubuntu count apparently in the other direction and the login dialog shows up on the other screen.
In my case, if I turn on my Mac Pro the left hand screen turns on and if I boot into Mac OS X the login dialog will be shown on the same screen. However, if I boot into Ubuntu the login dialog will be shown on the right hand screen.
I haven't been able to "fix" that and I had to drag-drop Gnome's top and bottom menu bars to the other screen. It's not a big issue though (just annoying).
sudo cp xorg.conf xorg.conf.bak
sudo aticonfig --dtop=horizontal
sudo aticonfig --dtop=horizontal,reversed