pilots of B17's flew manually when in the "box" formation.
Or any other formation. You won't use an autopilot when flying formation. "George" is great when you are alone in the sky, but he can't react to all the interactions when in formation with other aircraft. The exception to that is that the lead ship is often on autopilot.
When we do aerial refueling, we train with the autopilot on and autopilot off, which is to say that part of the time the tanker is on A/P and other times not. The receiver aircraft is always hand-flown. That's training. In the real world, the tanker is always on A/P, because that makes it a smoother delivery platform. The reciever is still hand-flown.