Instead of different sound cards, why not just get one with multiple I/O? You're opening yourself up to hardware conflicts running sound cards on two different busses (PCI and FW). I'd also reccommend that, if this is a PC, stick with PCI card interfaces. I've run USB and FW interfaces on numerous different platforms over the years - although they all worked, there were consistent and evolving, nuisance issues that popped up on each - most were traced back to bus-related conflicts. Conversely, the PCI card products that I currently use (Card Deluxe, Lynx, EMU) have been solid.
Speaking to your other question - all of the I/O's on your machine will show up when you cfg recording channels. Provided that both AA and Reason will play nice with each other (i.e. releasing the drivers when not in-use), then the cfg you select initially in each application should come up each time the program is launched. Remember though: you could only have one software app running at at time, though (I think?).
Perhaps the bigger question though: why not standardize on one editing platform and save yourself some possible grief?
-D