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I'm not completely sure what's going on here. fglrx properly supports xrandr and uses the Xorg XINERAMA extension to describe monitor placement for the window manager. So this is likely due to some quirk of the hybrid graphics, or maybe something with your xorg.conf file. I'd be interested in knowing if this xorg.conf file works correctly for you:
Unfortunately, then, I'm not sure what's going on. I know that the fglrx drivers keep some configuration in /etc/ati/amdpcsdb but I don't know of anything in there that would cause your XINERAMA extension to display the wrong information.
Start it up, click on 'Display Manager' under the 'Pages' section, and both your monitors should be listed.
If you then switch to the 'Multi-Diplay' tab, it should allow you to configure your multiple monitor setup, the default seems to be cloned displays, this might be your problem. Change the selection in the drop down list to switch away from cloned.
It does require a reboot (or restart of X) to enact though.
This is the way I've always done it, never needed to mess with the X configs, hope it helps...
mysql_connect: Sorry, I obviously misread your first post.
The only other thing I can think is that you are running amdcccle without root privileges, or that you haven't run aticonfig yet (which has already been suggested). I assume there is nothing helpful on the 'Switchable Graphics' screen.
Either way, it doesn't seem like its to do with that utility anyway, more to do with X, and I don't have much experience in that area.
Sorry I couldn't be more help, hope you find a solution soon.