Setting up an Xbox 360 controller to only work on one screen

What I would like to do is be able to use an Xbox 360 controller to issue commands to only my main character. I have setup the controller in game to tell it what to do (Y is jump on the controller and spacebar is jump on the keyboard for example). Currently I can use the controller in game but it sends commands to all three of my characters as if repeater was turned on but only sends commands to my main character if I use the keyboard. Can anyone tell me what I need to do to get the controller to only send commands to my main character?