I have followed a few guides to the T and I have ONLY roms inside of my retropie directory. Nothing else. The last guide I went off of is http://supernintendopi.wordpress.com/ . At first I used the RetroPie Project SD Card Image and thats when I noticed it first. So I decided to start over and do it the very long way to still find no directories. I can get into emulationstation and I have all the roms showing in SNES I also can open the games and hear them but I cant control them at all. I can control emulationstation though. The step I continue to get stuck at Configuring Controllers and Other Settings.
./retroarch-joyconfig >> ~/RetroPie/configs/all/retroarch.cfg
BTW I have a USB SNES controller.