Okay, when I first got mupen64plus and tried to use the code they gave here: http://code.google.c...ControllerSetup, it made the controls a little wonky, so I decided to change the numbers around and presto! I got the controls to where I want them too, if you have a GP Pro USB controller, I think you might find this useful:
; InputAutoCfg.ini for Mupen64Plus SDL Input plugin
[GamePad Pro USB]
plugged = True
plugin = 2
mouse = False
AnalogDeadzone = 4064,4064
AnalogPeak = 32768,32768
DPad R = hat(0 Right)
DPad L = hat(0 Left)
DPad D = hat(0 Down)
DPad U = hat(0 Up)
Start = button(9)
Z Trig = button(7)
B Button = button(2)
A Button = button(1)
C Button R = button(3)
C Button L = button(0)
C Button D = button(6)
C Button U = button(8)
R Trig = button(5)
L Trig = button(4)
Mempak switch =
Rumblepak switch =
X Axis = axis(0-,0+)
Y Axis = axis(1-,1+)