I'm no expert, but I think RetroArch can only have one mouse index per player. So I don't think you can assign two of these devices at the same time through the menu. If it were possible to somehow make the operating system see two input devices on the same device index that would be one way. I have no idea how to do it though.
I think as painful as it may be, the only thing to do is assign whichever device the most games use as the default and then create game specific overrides for those that use the other device type.