Showing the directory structure of RetroPie 2.3 (not massively different for 2.6.0 etc..) and where config files are used. Should help manually make edits if required.
Shows where the game metadata is stored as well as controller configs.

Some more path info here:
http://blog.petrockblock.com/2014/07/01/major-update-for-retropie/

Also a reference here to how RetroPie/RetroArch automatically use controller configs:
http://blog.petrockblock.com/2013/12/02/retropie-autoconfig-functionality/

Default RetroArch file here:
https://github.com/libretro/RetroArch/blob/master/retroarch.cfg