Hi @sniktun
Don't worry, we all have to start somewhere.
First of all, when you load the game, it says to configure press a button. If you press a button here, it will take you to the options to change which emulator it uses.
I think Mupen64-Glide is normally the default. lr-mupen64plus is not the same as Mupen64, it is the RetroArch port of mupen64 and uses a different video driver.
If you want to add extra emulators to the system, the easiest was to do it is from the RetroPie-Setup in the retropie menu. This is also where you can update the emulators to the latest supported version.
If you need further assistance, I would suggest completing the details in https://retropie.org.uk/forum/topic/3/read-this-first so that we have all the information on your setup.
Si