Adding a New Controller
So you got your hands on a shiny new controller. So how do you configure it to work with RetroPie? Simple, just follow this guide. If your new controller is wired or wireless, just plug the usb cord or dongle in to the back of your Pi. If you have a bluetooth controller, you'll first need to pair it with the Pi. For instructions on pairing a bluetooth controller, CLICK HERE.
CONFIGURE YOUR CONTROLLER
Once your controller is plugged in (or paired) you'll need to press START on your current controller and select CONFIGURE INPUT. It will ask you if you're sure, say YES. This will open the controller configuration menu. You can also access this by restarting the system with only your new controller plugged in and it will automatically load the controller configuration menu.
Simply follow the on-screen instructions and press the buttons the menu requests. If it asks for a button your controller doesn't have, press any button on the controller and hold it for a couple seconds and it will skip the assignment. When it reaches the end, the last button will be for the HOTKEY button. This is usually set as the SELECT button on your controller.
Press OK and you're done.
If you have two (or more) of the same controller, you'll only need to configure one of them and the rest will work from that one configuration. To learn more about controller configuration, please read the official documentation HERE.