After manually looking through the file system at various locations, i think i got it resolved.
In order to get the mupen64 controls to match up to my uxb n64 controller, i had to make the changes in a different file:
First, the file system is read only, so you have to make it writable by running the following command:
mount -o remount,rw /
then edit the following file:
/recalbox/share/system/configs/mupen64/InputAutoCfg.ini
add the following text:
[Generic USB Joystick ]
plugged = True
plugin = 2
AnalogDeadzone = 4096,4096
AnalogPeak = 32768,32768
Mempak switch =
Rumblepak switch =
mouse = False
A Button = button(6)
B Button = button(8)
C Button R = button(1)
C Button U = button(0)
C Button L = button(3)
C Button D = button(2)
DPad D = hat(0 Down)
DPad L = hat(0 Left)
DPad R = hat(0 Right)
DPad U = hat(0 Up)
L Trig = button(4)
R Trig = button(5)
Start = button(9)
X Axis = axis(0-,0+)
Y Axis = axis(1-,1+)
Z Trig = button(7)
This will set your controls properly. THen you will most likely run into issues with hotkeys. As it turns out mupen64 has it's own hotkeys that are separate from the default ones. to change them, you have to edit the following file:
/recalbox/share/system/configs/mupen64/mupen64plus.cfg
look for the section titled
[CoreEvents]
locate the joy mapping shortcut you wish to disable and change the value to ""
for example, to disable fast forward, find this:
Joystick event string for fast-forward
Joy Mapping Fast Forward = "J0B4/H0V2"
and change it to:
Joystick event string for fast-forward
Joy Mapping Fast Forward = ""
repeat for all hotkeys you wish to disable. (screenshots and save states were really messing with mine)