Groups are just helpful if you have a lot of systems and want to separate them - like Arcade, Consolde, Handheld..
If your list isn't generating, are you sure your roms are not in zip format (or 7z for that matter?) instead of nds files?
As long as you have the correct rom path, correct file extension and are using rom_folder to generate - it should pick up any files in that path.
Double check - when you copied the mame config folder, do you have the list ini files in there? those are the mame-0.ini, ... - rename mame-0.ini to whatever you named the system config folder, like gameboy-0.ini - that is the configuration for the main list. Also look in the mamewah\files folder and see if the list file is generated there - it would be something like gameboy-0.lst
If all else fails, see what the mamewah.log file says after you have tried to generate the list..