Complex sentence: The flight engineer is thus a integrated member of the flight deck crew who works in close coordination with the two pilots during all phases of flight, thus, the flight engineer position was usually placed on the main flight deck just aft of the pilot and copilot.
Split into simpler sentences: The flight engineer is thus a integrated member of the flight deck crew who worked in close coordination with the two pilots during all phases of flight. Thus, the flight engineer position was usually placed on the main flight deck, just to the aft of the pilot and copilot.