NeoGeo does run surprisingly well! Video should be up now, and glad I could help.
I have a video that goes into this, check around the 4:40 mark: https://www.youtube.com/watch?v=lh0n5PWN2lI
What you need to do is access the F1 menu in the emulator, go to settings then input settings -joypad mapping. Select User 1 Bind All and go through the button assigning. It wont actually ask for n64 buttons but I can tell you that the C buttons are mapped to the right analog stick; so when it asks for Right Analog Y- (Up) you would press the C-Up key on your gamepad.
Hope this helps, let me know how you go.
YouTube is a bit slow processing today but I made a quick vid to show you how it runs. Raspberry Pi 2, Mame4All, running Pi2 overclock which is only a modest overclock (100Mhz). Check back at this link it should be up anytime now: https://www.youtube.com/watch?v=feEF4RHFkok
*edit* It does seem to run quite well, and please excuse my appalling skills.
Hi typedan, what version of retropie are you using?
If you are using 2.6 your es_systems.cfg will be located in /etc/emulationstation/ check out this vid if you need help: https://www.youtube.com/watch?v=2WGpGCn9NeI&t=91
Once in, you can find the playstation section and delete the .bin .BIN from between the <extension> tags and they will no longer show up. You can see it in the same video at 1:56.
Another good command in linux is find. Type ‘sudo find / -iname es_systems.cfg’ and it will locate all copies of it for you. Hope this helps!
this video goes over it very quickly: https://www.youtube.com/watch?v=prCRRlZ3Ngk
Good luck!