IMO, the quickest for your situation is to use one of the ctrlr files that comes with mame ( mameUI only has a sample that doesn't have a neogeo input set ). Ctrlr files can change the inputs for all games, specific games, a parent and it's clones, or all games that share a driver file; all neogeo games share the same driver. I suggest trying hotrodse.cfg or xarcade.cfg.
Next might be hand editing one of mame's ctrlr files; Edit the "system=default" for all games, and the "system=neogeo" for neogeo games.
You could also hand edit the sample ctrlr that comes with mameUI, but it's almost easier to start a a new ctrlr file fresh. Rather than repeating it, here's our
ctrlr file wiki page; I'll gladly help if that's not clear.