And just to elaborate a little more
<sdcard>/Android/data/paulscode...
is a special folder, which Android automatically erases when you uninstall the game. We use that location for app files that the ordinary user should never touch. Rom databases, cheat databases, etc. We make it accessible though to allow the possibility for expert testers and developers to modify the data when debugging.
<sdcard>/mupen64plus/
is for user-generated data that should never be erased when you uninstall. Game saves, autosaves, slot saves, SRAM data, controller profiles, etc. In version 3 this will also include custom cheats, custom touchscreens, custom emulation profiles, cover art, and maybe more.
<sdcard>/mupen64plus/SomeGame.z64/...
is for manual saves related to SomeGame.z64 (the rom itself could be located anywhere). That way when you're in-game and you load a manual save, you see only the saves related to SomeGame.z64, and not SomeOtherGame.v64 or whatever. Simply naming the folder to match the rom name is not perfect though, and in version 3 the game-specific save directories will probably be structured and named a little differently.