You can edit using vi in the console.

vi ~/RetroPie/configs/all/RetroArch/retroarch.cfg
or if you have the newer RetroPie build…
vi /opt/retropie/configs/all/retroarch.cfg

This will bring up your config in the console.
Navigate to the place you want to edit and type ‘i’ to start editing.
When done editing, press ESC and type “:wq” this will write the file with your changes and quit vi.