The config file locations of all emulators are confusing. For example, the config file of dgen is stored under configs/all. The right path should be configs/megadrive:
$rootdir/configs/all/dgenrc should be $rootdir/configs/megadrive/dgenrc
Emulators like gngeo and gpsp or emulation station store there files under %homedir%/.<emulator> or in the application folder. It is possible to create symlinks under $rootdir/configs/<emulator>. $rootdir/configs/all/gngeo/<symlink to $rootdir/.gngeo/gngeorc> $rootdir/configs/all/gba/<symlink to $rootdir/emulators/gpsp/raspberrypi/keys.ini> $rootdir/configs/<symlink to $rootdir/emulators/RetroArch/config>
So every config file can be found at the same location.