(continued from last post)

after you type cd RetroPie-Setup

type:

./retropie_setup.sh

this will bring up a menu and you should select Update RetroPie Setup Script

when that is complete select SETUP(only if you have …)

then select Register controller for RetroArch emulator

with your keyboard and USB controller connected follow the prompts to setup your controller

Reboot the raspberry pi and configure the controllers within emulation station.

I only did this for one controller and it worked for both within the NES emulator.

Hope this helps.