It’s a symlink to /opt/retropie/configs/c64 so you can just add it there.

You can use sudo nano newfilename

Or cat > newfilename

Or it’s editable over samba shares which may be an easier option.

https://github.com/retropie/retropie-setup/wiki/First-Installation#samba-shares-needs-an-active-internet-connection

But they should just be created when you save them from within the emulator.