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Hi retrofredde, try it:
While the Raspberry is powered off, plug in one of your USB controllers. You should also still have your keyboard plugged in.
Power on your Raspberry by unplugging it, and then plugging it back in again.
Your Pi should go through its regular startup, and launch EmulationStation.
Before we can configure your controller for working with EmulationStation, we need to get rid of the .cfg file which currently should be telling ES to work with your keyboard. So from the EmulationStation main menu, press F4 to get back to your terminal.

cd .emulationstation
sudo rm es_input.cfg

Note: If you want the ability to navigate the EmulationStation menu with more than one controller (2 Player), you should shut down your Raspberry Pi now, plug in your second controller, and then power it back on, and skip the next 2 lines.


Now, I can to navigate the emulator GUI with my pads.
I hope it helps you.