Did you get your controller working in the game? If not, follow these steps from the link Katamari posted...
Once you are done with this, it should boot up EmulationStation. You should now be able to use your controller to navigate the EmulationStation menu. Keep in mind that this is only the controls for the frontend, not for the emulators. We’ll get to that now.
Press F4 to exit EmulationStation and go back to terminal.
./retroarch-joyconfig >> ~/RetroPie/configs/all/retroarch.cfg
Next you are going to use your controller and follow the prompts. If your controller has less buttons than the config tries to setup (My SNES controllers lack the R2/L2, R3/L3, and Joysticks), then you need to select a dummy button (I used left trigger) for the buttons you don’t have. We will edit those out later. Once this is done, it will bring you back to the terminal.
At this point, you should be ready to game with one controller. If you type sudo reboot in your terminal, it should restart, and bring you into EmulationStation on the restart. You can then use the controller to select a game and play it. To setup a second controller, go back to your terminal (Esc to exit game, F4 to exit EmulationStation) and follow the next steps: