As you can see, the Select button mapping is chosen to enable hotkeys.
Also, this wont overwrite any you have already set, just add to it if you havent set them.
Obviously you could go in and manually change these if you want, but every time you register a new controller it will run again.
RetroPie help guides --> https://goo.gl/Yfy8kj
Please read this before asking for help --> http://goo.gl/eLErnl