I doubt many readers on this forum have ever used an Amiga machine, let alone have used any kind of Mac (PowerPC-based or Intel-based) with more than one graphics card installed... in the same machine. With that being said, I found some mention of other people on the Ubuntu Forums who also brought up the same topic:
However, you might be in a better position than the people there since BOTH of your graphics cards would end up relying on the same ATI driver (more or less), i believe. The main problem is whether or not Xorg will allow for more than one "Device" section in the same xorg.conf file.
While I was looking around, I also stumbled upon this exciting piece of info...:
And even if it's posted on the ArchLinux page, I believe Xorg is still Xorg for all intensive purposes... so why not try it out? By all means, let us know your findings!
But if I misunderstood what you really wanted.... like you really do WANT TO DISABLE either one of your ATI cards, then presumably, all you'd have to do is simply comment-out the corresponding device entry of the ATI card that you want to be deactivated in the xorg.conf file.