To switch between the two graffic cards you have to switch the main screen to the second and not simply change their positions.
To do this go to monitor preferences and drag the little white rectangle at the top of the main screen onto the second one.
It is really not recommended to use a pci card with the modul8 output.
I once tested it with pci cards and it jams the software (this is due to the weak bandwidth).
Although we haven't tested this, the pci should theoretically work fine for the user interface as there should not be any texture transfer once the interface is loaded.
Otherwise, if your AGP card has two outputs it is better to plug both the interface and the output into it.