It can't be done by now. I think using the controller for wii and GC interfere each other.... For example: in SMG i have configured my gamepad with the pitch and roll feature on the left analog stick. Running SMG all is ok but running a GC game the left stick not respond correctly.If I define the roll and pitch feature with the keaboard all is ok. Hope the dev correct this "Bug" (I know is not a real bug) in future disabling the wiimote controller when a GC game is running or with other methods.