About GnGeo-Pi and its controller setup. You can choose almost any button to activate the menu and set certain buttons on your Gamepad to be the “yes” and “no” to choose options in the menu (like Exit). This is my from my personal tips and hints text file, hope it helps:

About GNGeo-Pi:
~~~~~~~~~~~~~~~~~
Emulator used: GnGeo-Pi. See https://github.com/RetroPie/RetroPie-Setup/wiki/neo-geo. Once you’ve started GnGeo-Pi at least once a file called gngeorc will be created here:

/home/pi/.gngeo/gngeorc

For more info about the config file, see: https://github.com/ssilverm/PiMAME/blob/master/.gngeo/gngeorc.

Example, my /home/pi/.gngeo/gngeorc file:

# Meaning of the code:
# Kxxx : keyboad key number xxx
# JxByy : Joystick number x Button
# JxAyy : Joystick number x Axe yy (use a lowercase ‘a’ if you need to invert the axis)
# JxHyy : Joystick number x Hat yy
p1control A=J0B0,B=J0B1,C=J0B2,D=J0B3,START=J0B9,COIN=J0B8,UP=J0a1,DOWN=J0a1,LEFT=J0A0,RIGHT=J0A0,MENU=J0B7
# system type? arcade or home
# ‘home’ doesn’t seem to work…
# country?
# japan, usa, europe
rompath /home/pi/RetroPie/roms/neogeo

About Joysticks:
~~~~~~~~~~~~~~~~~~
Config files -> Joystick configuration is vague and complex. The following config files are but a few:

[1] /opt/retropie/configs/all/retroarch-joypads/ThrustmasterTMiniWireless.cfg
[2] /opt/retropie/configs/all/retroarch.cfg
[3] /opt/retropie/configs/nes/retroarch.cfg (EXAMPLE)
([4] /home/pi/.emulationstation/es_input.cfg )

Button codes -> Find the numbers for the various buttons on your particular gamepad in [1]. File [4] seems to be an over ride. Example of gamepad entry fot the Nintendo NES in file [3] [https://github.com/RetroPie/RetroPie-Setup/wiki/RetroArch-Configuration]:

input_player1_a_btn = 0
input_player1_b_btn = 1
input_player1_y_btn = 2
input_player1_x_btn = 3
input_player1_start_btn =
input_player1_select_btn =
input_player1_l_btn =
input_player1_r_btn =
input_player1_left_btn =
input_player1_right_btn =
input_player1_up_btn =
input_player1_down_btn =
input_player1_l2_btn =
input_player1_r2_btn =
input_player1_l3_btn =
input_player1_r3_btn =

Test joystick/determine numbers of your buttons etc. [https://github.com/RetroPie/RetroPie-Setup/wiki/RetroArch-Configuration]:

jstest /dev/input/js0

Setup controller -> from command line:

sudo ~/RetroPie-Setup/retropie_setup.sh

and choose “Register Retroachch controller”.