Yes, it's all in the manual.
BTW, when you say "APM", I assume you mean ArduPlane, right?
Ardupilot Mega Mission Planner. I guess i should say Mission Planner instead. Thanks Chris, I read it over again and totally missed that one sentence in the manual:
" In the Mission Planner read the stored waypoints and let it reset home to the stored position (which will now be the airport in your Xplane simulator that you're flying from. " Yup feel like an idiot that I didn't see this sentence.