It was a difficult task, but I found the answer here: https://retropie.org.uk/docs/Nintendo-64/
What I do is I will configure via Retropie the config how I like it for all the general emulators and then i will edit the /opt/retropie/configs/n64/InputAutoCfg.ini file with the below which as long as your using the USB N64 pad should get your 64 controller mapped correctly. This works for the “iNNEXT N64 Controller” aswell. Just Label the “[Generic USB Joystick ]” as “[DragonRise Inc. Generic USB Joystick ]”
[Generic USB Joystick ]
plugged = True
plugin = 2
mouse = False
AnalogDeadzone = 4096,4096
AnalogPeak = 32768,32768
Mempak switch =
Rumblepak switch =
R Trig = button(5)
Start = button(9)
Y Axis = axis(1-,1+)
Z Trig = button(7)
DPad U = hat(0 Up)
A Button = button(6)
DPad D = hat(0 Down)
X Axis = axis(0-,0+)
DPad R = hat(0 Right)
B Button = button(8)
DPad L = hat(0 Left)
C Button R = button(1)
C Button L = button(3)
C Button D = button(2)
C Button U = button(0)