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The auto config files are in
/opt/retropie/emulators/RetroArch/configs
They relate to the specific controller you are using – you can tell which has been configured by looking at the last edited date (the comman is: ls -lah)
The retroarch.cfg file will import those settings. Or you can type them in the retroarch.cfg file manually
/opt/retropie/configs/all/retroarch.cfg
Search the file for the text ‘joypad’ its towards the end and has examples in there – just under the keyboard config section. The above video should show it.