Finally got some time to look at how Powermame does the GPWiz config, and it's something that shouldn't be too hard for Youki to add, (if he wants to), but not just a quick fix. The problem is that if you switch games from one setting to a different one, there isn't an easy way to update the GPWiz.
If I understand it correctly, Powermame internally sets what type of controls each game has (at least 800 of them anyway - the rest use the default setting) and when it runs a game, it queries what type of control it is. Based on which one it is, it then sets the mode before starting the game.
The problem with firing off an executable before the game with Atomic is that you are stuck in that mode. The only way around this I can see with Atomic the way it is is to manually set each game by specifying a unique command for each rom.
I suppose you could add support for a couple and do the old notepad find and replace method, but there doesn't appear to be an easy way to add this.
It's all up to Youki!
