pretty sure you'd be into different windows configurations, which becomes a pain with different graphics cards.
what might work is having different windows installations,and selecting both the graphics card [agp/pci] as well as the boot disk:
option 1: select pci graphics card in bios, boot hard disk 1, disable agp in windows
option 2: select agp graphics card in bios, boot hard disk 2, disable pci graphics card in windows
as soon as you forget to make one setting or the other at boot, expect annoying problems.
and it may not work anyway if you get those unreported resource conflicts.
might need to mess about with a boot manager too, to make sure the right disk is set active.