Curis,
You only need to send the APB sentence to your autopilot. The reason the BWC sentence always contains a waypoint of 0 is that some of the early Autohelm units would not work when sent an actual waypoint number. Also some units cannot handle waypoint numbers that exceed 20 or 30.
The autopilot should work just fine with only the APB sentence being output.
-Justine Baldwin
Technical Support Specialist