Hi Amaryllis,
Here's how I do it:
1: load up a neogeo game, set up the inputs and dips up as you'd like
2: in the input editor (F5), press the [Save Preset] button
These new settings will take effect for any NeoGeo game that hasn't been run yet. For games that use the old settings, you can do either:
A: go into directory config/games and delete the .ini file for each NeoGeo game -or-
B: from the input editor (F5), first pull-down select "Player 1", second pull-down select "neogeo", then click Use Preset
This same method can be used for other systems, like NES or Megadrive, except option A is a lot easier, as the input/dip config filename is prefixed with nes_ or md_.
best regards,
- dink