Yes. You can create a "SNES" emulator for snes9x and a "SNES2" emulator for RA. Then you can just change the SNES games that you want to use RA by editing the romlist.txt "Emulator" field from "SNES" to "SNES2". Of course this is just an example and you can call the emulators anything you want (i.e. SNES_snes9x, SNES_RA, etc.).
If you use the GUI as I mentioned above, this will be the only change in any file.