There's no reason using the same emulator it shouldn;t work. When trying it, make sure both roms are named the same and that your using an emulator version that reads full rom names. Then make sure you save a file on both platforms first, Then change the savegame name accordingly. As long as you are using the same name of the rom on both platforms it should not change the name of the savedgame (as long as the emulator is the same PC SNES9X, Wii SNES9X).