The games are already set up to emulate the original control panel of each of the original arcade games, so generally there is no need to change them. You can change the controls for any game by simply pushing the "Tab" key while a game is already running to access the controls menu. The Input (this game) overrides the general input settings and adds custom controller settings for just the game being used. Input (general) option allows controller settings to be applied to all games (not recommended).
If you accidentally change the controls under Input General, you can fix this by simply deleting the file C:\Max 2.10\MAME\cfg\default.cfg.