EMUNAND are generally compatible with either card, with the caveat that Emunand 8.x currently only works with GW.
Also your MT card saves all your game saves on the microSD card (using rom_filename)while the GW saves them on the 3DS SD card (using the game ID). You can use your MT saves but you will need to move them to SD and rename them.
Other than that just change the launcher and roll.