I have this Asus Pundit system at work. I put in an old S3 VGA card to use dual screen mode; as that card did work, but only'd give me 640x480, I exchanged it for a Matrox Mystique card. I can get the Matro x card to work, but not when using the onboard VGA on the same time. If I toggle the BIOS option to make the PCI VGA the initial display (instead of the onboard VGA), the Matrox works. Otherwhise the Onboard ATi works.

When booting, I get an error message saying "PCI: Cannot allocate resource region 0 of device 0000:02:0e.0". The PCI addy is the addy of the Matrox card. When I configure the Matrox to be the first card, I get the same error, but with the address of the onboard card.

I tried numerous BIOS settings (ACPI etc etc etc) but none works. This problem occurs on both Ubuntu 5.10 and Knoppix 4.0. Any ideas?

This howto might give you an idea where to start.
http://www.faqs.org/docs/ethernet/Ethernet-HOWTO-9.html
If you can determine the kernel modules used, you can change the iobase address for built in devices giving a boot option, or if it is a module, you can supply that information in modprobe.conf.

A kernel module sometimes has a text file in the kernel source which lists options that can be used.
Be sure to back up files you change and be prepared to use a rescue disk to boot up with in case the changes cause the computer to freeze.

You could also try reserving the io region of the built-in vga card. This may cause the other video card to get a different region.