You install retroarch from Gamestarter Repo as you usually install any other addons.....then from retroarch addon settings download core package and that's about it....you can basically forget about retroarch after setting it up if you r running your roms from AEL.
It's not an easy task as it might look to set everything up first time...If you r going to make AEL and Emulation Station with all the bells and whistles...artwork,logos,backgrounds for each game and so on it will take you some time..to give you an idea it took me over a week to set it all up...but after that you just save you roms and artwork and xml's in a safe place for future backup and restore...For AEL and ES you can use the same artwork folders...no need to duplicate any folders