Have you tried to configure it with the default Ubuntu "Monitor" tool or with the ATI Catalyst Control Center?
Last week I had the same problem and I solved everything installing the last driver from ATI and working with the configuration.
Here you can find the link to driver for linux
After you downloaded it you have install and open this program with root access.
In the "Display Manager" menu configure your monitors selecting the option "Multi-diplay desktop with display(s) 2" on your first monitor and "Multi-display with display(s) 1" on your second monitor. Apply the changes, log off and log in again. In every step of your configuration you find the id of your monitor in the left top corner of your display.
I tried also all the other options and I find out that "Multi-display with display...)" is the only one that suits my needs. Infact I tried also to option for two different monitors but I was not able to run an application in my main monitor. I tried also "two different monitor" + Xinerama and I had a lot of problems with application not running and so on. So I think that is the only option suitable for me. Let me know if you solve the problem with another option or configuration.