The BeOS will use the first supported graphics card it finds in your system. There is currently no way to configure which card will be found first, other than by swapping cards in their slots.
In other words, it's not a recommended configuration, but it should work. We'll certainly attempt to fix any and all bugs we can find that prevent this from working.
Note that some graphics cards will actually conflict with each other when installed on the same system (usually when one card is a clone of the other). This is a hardware-level conflict, and we can't fix those, so some graphics card pairs will be unsupportable, even with bug fixes.