Using the ATI control panel software - you can select how you want the dual head to be set up
You should have a line like this in teh xorg.conf assuming your using the fglrx drivers. If not - get them from ATi
Option "DesktopSetup" "0x00000201"
In that case, it sets up my dual head with my primary screen being on the VGA and on the left of the 2nd (DVI and right)