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That’s it exactly. The Gpioneer plays together with the USB controller just fine. It does not matter which GPIO inputs you use for your buttons, just make sure it’s an INPUT. The only thing that threw me with installing GPIOneer is it needs the rpi.gpio library installed first. Use the answer in this link: if you are not python smart.

Once installed, you just type in the URL of the pi, and it will bring up the GPIOneer configurator to program your buttons. What’s nice is you can change them at any time very simply. Your other choice is retrogame. It does basically the same thing as GPIOneer, but it is not as flexible.