There are a couple things I'm confused about in your post... I will ask you about them, and also point you to a resource that might help you fix it on your own.
There is the option to chose between PCI and VGA in the BIOS
Do you mean PCI and VGA or PCI and AGP? Both of the cards will support VGA mode.
if I boot into windows with the PCI selected things work fine and Windows uses the VGA card as the primary screen (it switches control over from the PCI card)
Are you talking about MS windows, as in a dual boot system, or are you talking about X Window system?
Now, here's my advice. Check out this howto :Xinerama howto
. There's sections in here about scanning the bus so you know the addresses of your video cards and how to tell XFree86 which card to use. You should even be able to use both cards, if that's what you want.
Hope this helps.