Okay so if you did not set the bios option before you installed the first time then I could see why you are having this problem. however if you are absolutely sure you set the bios option before installing CCC the first time then I would start to think there is something wrong with your board. Do you remember if you changed the dual view setting before installing any drivers?
Also the GPU is installed into PCI Express lane one correct? Its the one closer to the CPU.
If you did installed CCC with the wrong bios setting or in the wrong lane then I think if you follow the uninstall process we can get it to work.
Uninstall CCC driver then turn your machine off remove the GPU. Power up and verify that the APU is showing up as a new hardware device and then power down. Reinstall you GPU in lane one. Power up into bios make sure dual view is selected and save the setting. Start up your computer APU and GPU should both be new hardware devices install CCC. It should work now.
Also you need the catalyst profile download as well to have dual graphics work.http://sites.amd.com/us/game/downloads/pages/crossfirex-app-profiles.aspx
Let me know if this has helped.