I don't envy you, this journey you have chosen, but I believe you will enjoy the end result.

This doesn't have much to do with gngeo. It has more to do with the current state of the dumped ROMs.

I can tell you what I did.

First, I installed gngeo on my desktop. I decided to make it work there first. And don't mess with any frontends until you get it working in command line.

I recommend getting it working on your desktop first.

I made sure I have a directory for my ROMs, and I have a directory inside that directory called "bios".

In the "bios" directory, I have the extracted BIOS files.
My gngeorc file (in the hidden .gngeo directory) has the lines:

rompath /media/mmc1/roms/neogeo
biospath /media/mmc1/roms/neogeo/bios

Here's where the problems start. There are numerous versions of BIOS files and numerous versions of ROM dumps. There are old dumps and new dumps. There are MAME dumps and NeoRage dumps. It's a mess.
All I can say is keep looking and try different combinations. I think you want the MAME versions, but just keep trying.

Try command line, something like:
gngeo -B /media/mmc1/roms/neogeo/bios -i /media/mmc1/roms/neogeo joyjoy

I can tell you I went through several bios zips before I found something that worked.

Here's an interesting part. If I enter the above line, it works. If I enter:
gngeo -B /media/mmc1/roms/neogeo/bios -i /media/mmc1/roms/neogeo joyjoy.zip

.. it doesn't work. It's very picky. You might want to include the .zip, but don't.

Good luck.

desiv