In AUTO mode the follow a mission (a set of GPS waypoints and other commands) set by your ground station configuration. When entering AUTO mode ArduPlane will continue from whatever mission item it was last doing, unless you have reset the mission.
When in AUTO ArduPlane will by default allow the pilot to influence the flight of the plane by using “stick mixing”, which allows for aileron, elevator and rudder input to steer the plane in a way that can override the autopilot control. Whether this is enabled is determined by the STICK_MIXING option. By default stick mixing behaves the same as FBWA mode.