Didn't you already asked this a couple months ago ?
You got an answer on how to set-up your keys in Emulationstation - did you try applying the steps there to configure your controller ?
Another question: can I switch of the emulator type display in favourites, that thing in brackets:
MOON PATROL [MAME-LIBRETRO]
I think this should be possible for custom collections, though your version of Emulationstation is a bit old for that. How did you install RetroPie ?