Mayflash Controller Setup

I must be missing something. So I have a Mayflash N64 Controller Port + Mayflash Super Nintendo Controller Port. I’m able to get the gamepads configured to see what button goes where. However when it comes to playing a game on one of those controllers, it defaults to the Xbox 360 Controller I have plugged in. I looked around to try to figure out how to set the controller I want to use on the game but I am unable to find anything on how to do this. Any clue on how to setup a game to use a specific controller?

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