There should be no issue as RetroArch should recognise each controller and load an autoconfig file when it detects the controller.
Plug in your iBuffalo pad and launch RetroArch, the OSD should display "USB,2-axis 8-button gamepad" on the screen. Go ahead and bind all your inputs for the pad, ensure that the option to load autoconfig is enabled and choose Save autoconfig file. Now, whenever you start RetroArch with that gamepad plugged in, it should load that autoconfig file.