I have only run two-display systems with two video cards. At work, I have the onboard Intel i810 AGP and a Matrox Millennium PCI powering two NEC E950s. At home, I have a Creative Savage4 PCI and an ATi Xpert128 AGP powring a KDS VS-7e and a generic 17" monitor.
The key to your success will rely on how flexible the drivers for each of you cards are. Some drivers require that a card be used as the primary display only, while some other drivers will not work in a multi-display at all. These cases tend to be isolated to older cards are really aren't supported by the manufacturers any more (i.e., not still working on drivers).
-SUO