What I mean is this:
Say I want to play a game that relies on analog, such as NFL 2K2 or driving game. My setup would still have the hacked pads plugged into 1 & 2 even though I wouldn't be using them, and I would use 3 & 4 for the regular unhacked pads.
What I want to know is if I used port 3 with a gamepad in a certain game, will I have to set it up again next time I play that game, or will it remember that I have Player 1 set up to use port 3?
Basically, ports 1 & 2 will always be connected to the hacked pads. 3 & 4 will be swapped between either original pads or keyboard/mouse depending on the game.