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Cool, glad you got it working :-) A lot of the emulators are Libretro cores which can be configured through the Retroarch frontend with retroarch.cfg
You may want to create custom controls for each emulator, place a modified retroarch.cfg in the respective emulator folder, e.g. for Megadrive/Genesis place in /home/pi/RetroPie/configs/Megadrive/ this will override the default retroarch.cfg in /home/pi/RetroPie/configs/all/
To determine buttons you can run jtest which should be installed already, if not:
sudo apt-get install joystick
Then run:
jstest /dev/input/js*
(replace * with the index your pad is assigned)
Other emulators have their own config files.
As for Duke Nukem and Game Gear emulators I don’t use either, so you’ll have to search that one. I’m sure you can run Game Gear roms through the Megadrive emulator though?
The N64 emulator requires the Pi to be overclocked and will only run a few roms at a decent speed.