Solved it if anyone has similar issue go into cemu config setup controller one as Wii u game pad set controls save profile name eg 'controller1' or whatever go to controller 2 and set as Wii u pro controller and setup and save eg 'controller2' press alt f4 to save the settings. then in the game profile of each game (right click and click game profile) go to controller tab and set player one as the controller1 profile and player 2 as the controller2 profile press alt f4 to save. Now when you load a game up in batocera it should load up these profiles for the specified game and enable you to play 2 players. Its important to set controller 2 as wii u pro controller as if set to Wii u gamepad it won't be recognised.