i dont know if this helps, but i discoverd it when setting up my x-arcade controller.
in mame, you can tell it you are using a specific controller, which then remaps the keys to match up with that controller (x-arcade, hotrod, slikstik, etc). these profiles are located in your mame\ctrlr directory. in there there are .cfg files for the different controlls. if you look at the hotrod or x-arcade files, you will see towards the bottom that you can specify a different button layout for neogeo games.
so all you have to do is modify this to match up with your button layout and save it, then tell mame you are using that type of controller.
for example...
if you have buttons
4 5 6
1 2 3
4
you can let most mame games function that way, and when you play a neo geo game, it will automatically change to:
x x x
2 3 4
1
i may not have explained it very well, but if you look at the .cfg files, i think you will understand.
I am in the process of redesigning my control panel as we speak, and i am debating if i should add the neogeo button, right now i just have
1 2 3
4 5 6
i use that for all games, including neogeo..i dont really find it difficult to use, but then again, i never really played many original neogeo arcade games.
for those of you who do have them, is it worth doing? or should i just keep it the way it is?