While trying to be helpful, the above posts were not specific enough.
Using hints from the config files here:
/opt/retropie/configs/n64/InputAutoCfg.ini
/opt/retropie/configs/all/retroarch-joypads/WishTechnologiesAdaptoid.cfg
And the official documentation from both mupen64 and retroarch, I managed to create a configuration specific to the N64 controller with adaptoid USB<->N64.
(EDIT: The below confusion caused by one simple issue. One cannot restart emulation station to reload the /opt/retropie/configs/all/retroarch-joypads/, one has to restart the entire RPi!!! What a bug D:)
There is some confusion for me that I'm trying to work out. I set the save/load state, but somehow load state on button "12" and in the mupen config it's "DPad L = button(12)", yet start+C-left will load state... Weird stuff all around.
In WishTechnologiesAdaptoid.cfg:
#Start button
input_start_btn = "8"
#Start is now the "hotkey"
input_enable_hotkey_btn = "8"
#Left shoulder "L"
input_l2_btn = "6"
#Start (hotkey) + Left-Shoulder will exit the emulator
input_exit_emulator_btn = "6"
Full adaptoid config in /opt/retropie/configs/n64/InputAutoCfg.ini
I was using this to reference what button is what for the above changes. By default from the previously linked config, it had some issues, such as A button was C-down, C-down didn't do anything.
; Wish Technologies Adaptoid_START
[Wish Technologies Adaptoid]
plugged = True
plugin = 2
mouse = False
AnalogDeadzone = 4096,4096
AnalogPeak = 32768,32768
Mempak switch =
Rumblepak switch =
C Button D = button(1)
C Button L = button(4)
Z Trig = button(9)
Start = button(8)
Y Axis = axis(1-,1+)
DPad U = button(10)
C Button U = button(5)
B Button = button(3)
A Button = button(0)
DPad D = button(11)
X Axis = axis(0-,0+)
R Trig = button(7)
DPad R = button(13)
DPad L = button(12)
C Button R = button(2)
L Trig = button(6)
; Wish Technologies Adaptoid_END
Side note, I wanted to make sure keyboard and other controllers are disabled. I have some USB SNES style controllers, but I don't want them working with the N64 emulator.
In /opt/retropie/configs/n64/InputAutoCfg.ini
Find the "plugged" option for keyboard and other controllers you don't want to run in the N64 emulator, and change "plugged" from "True" to "False"
; Keyboard_START
[Keyboard]
plugged = False
#My case has these other USB controllers configured:
; 2Axes 11Keys Game Pad_START
[2Axes 11Keys Game Pad]
plugged = False