Ctrlr file.
That's how the x-arcade & hotrodse do it. (Check out the files in the ctrlr file if you use mame; mameUI does NOT include the files.) It's easy, but quite a few steps to make your at first; once set up, you can continue using the ctrlr file (unless mame changes it again, of course).
How to make a ctrlr file (lines starting with "*" are optional):
- *delete cfg/default.cfg
- *start any game in mame
- *do all every-game remaps (tab, Input (general), etc)
- *exit mame
- copy cfg/default.cfg to ctrlr/yourname.cfg ("yourname" is any name you want)
- edit mame.ini and set "ctrlr yourname"
- delete cfg/default.cfg
- start any neogeo game (<--- if repeat, start again here)
- remap for neogeo, except remap in the "Input (general)" menu, like you did for every game above.
- *
play game, err, test inputs 
- exit mame
- open cfg/default.cfg in a text editor
- find the line that starts "<system" and change the name from "default" to "neogeo"
- copy starting from "<system..>" to "</system>" (including these lines)
- open ctrlr/yourname.cfg in a text editor
- paste the lines after the last </system> already there
- save ctrlr/yourname.cfg
- delete cfg/default.cfg
- *repeat for other driver sets, parent/clone sets, or specific games.^
- test neogeo and non neogeo games
^ Change the system name to the driver, parent, or specific game name instead of "neogeo". And always order the systems with "default" first, then the drivers, then the parents, then the specific games last.
Note to self: come on reb, wiki this already.
