My controller has controls for 2 players, plus extra buttons in a separate location labeled A, B, A2, B2. There's also a section with 10 other buttons, with some labeled Select (generally the hot key, too), Coin One, Coin Two, Player 1, Player 2, Menu, Pause, and Exit.
What I was thinking was that it would be nice to use the extra four A, B, A2, B2 buttons for the controls in EmulationStation. Menu could replace Select-Player1 and pull up that menu, and Exit, of course, would drop into the command line (or maybe reboot).
From what you're saying, it sounds like I can do this by manually editing es_input.cfg - as long as someone doesn't come along and clobber that config with a new one. (But, of course, I'd keep a backup - and when I have people over, I put it in Kiosk or Kid Mode.) Then I can also edit retroarch.cfg separately for the emulators (other than ones like AdvMame, that use their own configuration file).
Am I right about this? (I want to make sure I'm clear and understand what you're saying.)