In the aircraft guidance-system design-process, a number of autopilots are designed at certain flight conditions. An autopilot is responsible for a certain task not the whole mission, e.g., an autopilot can be responsible for the a/c to have a certain rate of climb, velocity, or altitude…etc. And a need arises for a supervisory control system that manages the engagement and disengagement of each designed autopilot, passing the command inputs to them for the a/c to accomplish the whole mission. It looks like the supervisory control system existing in DCS's (Distributed Control Systems). In this paper, the logic of the online-software for such systems is presented, clarifying the inputs, outputs, and timing of the system. Also the logic of the Ground Control Station (GCS) software is presented. A realistic mission is adopted to clarify the operation of the guidance system.