Instructions
Purchase an adapter. In order to fully convert your SNES controller for USB usage, you have to purchase an adapter. Adapters such as Nintendo's SmartJoy adapter, converting your SNES controller.
Plug it in. Connect the end of the SNES controller into the box of the adapter (the way your would normally plug your controller into your SNES system). Place the other side of the adapter into your computer (the USB side).
Configure your controls. Once you have the emulator up and running, you have to go to the configuration menu (located at the top of the emulator) and figure out what buttons you want to correspond with each action. For example, the directional pad should be set up as your up, left, right and down buttons.