Hotkey+x will open the retroarch menu while youre in game. Then go to controls and remap as you like and then you can save it as a core remap. Remapping here won't influence your mappings in the standalone emulator because it doesn't use the retroarch controls.
I don't know if this is the best way, but I did figure out how to change it for this game and disable RetroArch saves to eliminate accidental overwriting. In case anyone else needs this in the future:
Create config file based on instructions from here, name will be [ROM NAME with Extension].cfg
In that file paste the following with the hotkey button of your choice:
#Change Hotkey for this game only
input_enable_hotkey_btn = 3
#Disable RetroArch saves
input_save_state_btn = null
input_load_state_btn = null
# Never save-on-exit after an override config
# or the override will make into the core config.
config_save_on_exit = false
The default N64 emulator is 'mupen64plus-GLideN64'.
What you want for Ocarina of Time is 'mupen64plus-gles2rice' You might even be able to use 'mupen64plus-gles2rice-highres' (I use the highres version). It plays well with this emulator, but not as well as Majora's Mask.
For Majora's mask you can just go straight to 'mupen64plus-gles2rice-highres', some slight slowdown in the town itself, but flawless everywhere else I could get to in my 2 hours of testing when I was configuring my N64 games a few weeks ago.
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.
@phrazelle awesome! I will have to download it when i get a chance. I saw your cabinet a long time ago and so badly wanted this theme. Now i can finally have it. Your nes arcade is way too cool. I cant get over it. The nes is my favorite system. Awesome stuff you have done.