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yes. you'll only have one system available outside of X, but inside yes, they should work together fine. i have a dual head agp/pci system running like a charm. I guess all you'd specifally need to do with the two cards is to state the physical location of the cards in your XF86Config rather than letting X find them themselves, as it's not guarenteed to find them easily.
I'd also say that Xinerama is annoying. i don't use it, and instead run two copeis of blackbox, one for each head. I can't drag windows between the two (the mouse still goes from one to another of course) BUT i have seperate workspaces on each one, so i can change workspaces on my main headm and not have a singel thing change on the secondary head, which i typically use for IM, watching films, or checking email.
any other questions..? well... someone else can answer.. it's 3am, off to bed.
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