To get the wireless XBOX 360 controller to function properly start the game and do not turn the controller on until you get to the "Play Ball" screen. You will then have a 100% working controller.
EDIT: In order to get your main profile to load and be attached to the controller the easiest method is to actually start the game with the wireless XBOX 360 controller on and then wait until the game loads to the "Play Ball" menu(the team selection screen) and then turn the controller off(take the battery pack out) and turn the controller back on and you will have a 100% working controller. If you do not do this then your original profile will be attached to the keyboard as an input device.
EDIT: In order to get your main profile to load and be attached to the controller the easiest method is to actually start the game with the wireless XBOX 360 controller on and then wait until the game loads to the "Play Ball" menu(the team selection screen) and then turn the controller off(take the battery pack out) and turn the controller back on and you will have a 100% working controller. If you do not do this then your original profile will be attached to the keyboard as an input device.