In order for the gamepad to be detected and configured by Emulationstation - and the other emulators - it must be detected as a gamepad by the OS. If the OS (Raspbian) doesn't see it as a gamepad, it means it's not compatible with Linux, so there's nothing to configure. I advise you to try another controller - if you bought this one specifically for RetroPie, then you should return it and get a better supported controller.
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