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If you want to set controls in a libretro based emulator, you can either update controller config file, or update the system specific retroarch.cfg

I wouldnt recommend updating the main retroarch.cfg (in the /all directory) for controller updates.

If you look in the /opt/retropie/configs/{systemname}/ directory, you’ll see the file that was created when you saved from the RGUI interface (do “ls -lah” and itll be the latest datestamped one). If you post that up here I could point out the section to paste in your /opt/retropie/configs/{systemname}/retroarch.cfg file.

This video gives an overview on where to change these files (although its a little out of date in terms of some of the paths – new one coming soon!)