It looks like I didn’t fully understand how templates worked. Sorry, I just got my controller the day I posted this and your reply helped me understand everything now. I wasn’t making templates so I was just using the base configuration. When I’d change that, it would change the base configuration universally. Now I created a RetroArch template and every time I open a new game I load it up first thing. After that every time I load that game it loads the right template. Creating a Cemu one now for when I load WiiU games, etc etc.
Thanks again for helping. I’m loving this controller! And the plugin makes things 100x easier.