Do you use the libretro core? We can’t give support for the libretro core because it’s not in our code base yet and an unofficial port.
Please ask here instead: https://forums.libretro.com/
Adding games works like adding Roms (I guess): Add the game directory and launch it through the core.
Through Add Content > Scan Directory in the RetroArch GUI.
The RTP path was not overriden by the port therefore the folders are: /data/rtp/2000/ and /data/rtp/2003/.