@nightbirdmedia mupen64plus-gliden64 isn't a libretro emulator so you can't use the retroarch menu. The save states are not compatible but there are conversion tools out there if you have existing save files. The default save file location for standalone mupen64plus is a little weird but you can change it by editing your mupen64plus.cfg and pointing it to save to the rom folder.
@jojin Look in the Docs, there's sections for each emulator, look over the Getting starting guide, the Emulationstation pages, then later on you can take a look over the RetroArch and Advanced configuration options. Feel free to ask in the forums also, there's no wrong question (well, almost).
Also if anyone can maybe give some alternatives to bluetooth audio as the lag ain't great, that will be greatly appreticated!
There aren't many solutions out there and it seems this solution not only breaks other audio outputs but also is unusable due to the lag. I'm almost certain the Pi dosen't have enough horsepower to emulate games and stream bluetooth audio, as per the tutorial above I have completely removed it and I recommend that you should too. Let me know how you get on and if you find an alternative that doesn't stutter.