There is always an option for USB controller, just click the button on the right side of the main menu repeatedly to toggle input mode.
(USB Controller/Keyboard/Touchscreen)
For it to be recognized correctly on Windows you need to set up the endpoints according to this document:
https://drive.google.com/file/d/0BwSDHIR7yDwSOGhPMTFyWEpDVWM/view?usp=sharing
(There is also some general tips in the manual).