How can I configure the graphic options for Wii and GameCube separately?

[Super-M]

I can play Wii Games only with 1x interal resolution and without any fancy added stuff, but I'm able to activate much more enhancements for GameCube games.

Is there any way I can separate the configs without too much work? I was think about two config files that are valid per system and not per game or something like that.

Thanks for any help.