that is a global approach..once it is done once, it is done for all games if you do it under Input General.
the problem is that for player 1 button1 for example, by default will be like:
kbd Ctrl or Joy 1 button 0 or mouse b0 or gun 1 b0
or something like that. you need to go select that input, hit enter to change it, hit esc to make it blank, then set it just to the button you want to actually control it. do this for all of the player 1 controls and then you are good to go. the only way that wouldnt work is if you have already created a cfg file for a specific game that overrides it.