Autopilot:
The FlightGear autopilot system is introduced here: http://wiki.flightgear.org/index.php/Autopilot
A tutorial on creating new autopilots is available here: http://wiki.flightgear.org/index.php/Ho ... _autopilot
A reference on autopilot configuration is available here: http://wiki.flightgear.org/index.php/Au ... _Reference
Another introduction is available here: http://www.flightgear.org/Docs/XMLAutopilot/
Information on tuning autopilots is available here: http://wiki.flightgear.org/index.php/Au ... _Resources
Route manager:
The route manager system is introduced here: http://wiki.flightgear.org/index.php/Route_Manager
The inner details of the route manager implementation are covered here: http://wiki.flightgear.org/index.php/Ro ... _internals
The GPS implementation is documented here: http://wiki.flightgear.org/index.php/GPS_internals