In order to get three controllers aligned to the same team, do the following. Keep in mind that the 2nd player has to be using a wireless controller.

With all three controllers on, choose the same side with controllers one and two. During gameplay, press start on controller one and enter the menu.
Turn the second controller off. Then, with the first controller, head to settings and controller setup. Slide the third controller to the same side.
Go back to the start menu, and just before resuming gameplay, turn controller two back on (there should be a rumble on the second controller).
Changes will come into effect after the first play.