To setup your controller, edit the mupen64plus.cfg file (~/Library/Application Support/Mupen64Plus/).
Put this in the [Input-SDL-Control1] section of the file.
If you mess up, you can close the emulator, delete the file and restart the emulator.
[Input-SDL-Control1] # Mupen64Plus SDL Input Plugin config parameter version number. Please don't change this version number. version = 2.000000 # Controller configuration mode: 0=Fully Manual, 1=Auto with named SDL Device, 2=Fully automatic mode = 0 # Specifies which joystick is bound to this controller: -1=No joystick, 0 or more= SDL Joystick number device = 0 # SDL joystick name (or Keyboard) name = "Pro Controller" # Specifies whether this controller is 'plugged in' to the simulated N64 plugged = True # Specifies which type of expansion pak is in the controller: 1=None, 2=Mem pak, 4=Transfer pak, 5=Rumble pak plugin = 2 # If True, then mouse buttons may be used with this controller mouse = False # Scaling factor for mouse movements. For X, Y axes. MouseSensitivity = "2.00,2.00" # The minimum absolute value of the SDL analog joystick axis to move the N64 controller axis value from 0. For X, Y axes. AnalogDeadzone = "4096,4096" # An absolute value of the SDL joystick axis >= AnalogPeak will saturate the N64 controller axis value (at 80). For X, Y axes. For each axis, this must be greater than the corresponding AnalogDeadzone value AnalogPeak = "32768,32768" # Digital button configuration mappings DPad R = "hat(0 Right)" DPad L = "hat(0 Left)" DPad D = "hat(0 Down)" DPad U = "hat(0 Up)" Start = "button(12)" Z Trig = "button(6)" B Button = "button(1)" A Button = "button(2)" C Button R = "button(8)" C Button L = "button(0)" C Button D = "button(3)" C Button U = "button(9)" R Trig = "button(5)" L Trig = "button(4)" Mempak switch = "" Rumblepak switch = "" # Analog axis configuration mappings X Axis = "axis(0-,0+)" Y Axis = "axis(1-,1+)"