When you load a flight with the 707, all lights are turned off, autopilot is turned off, and of course, the flight plan is changed from Seattle to Felts. This is important (I forget why), so do not delete this flight!

This is a link to the topic where I asked a similar question as you: http://www.captainsim.org/yabb2/YaBB.pl?num=1298685571/all

If you scroll down (or it might be on the second page) you will find Mark's instructions on adding the GPS so you can update your route progress. Using the GPS and the Navlog, you can fully update the doppler navigation system midflight (if you save your flight and come back to it later and your doppler settings are gone). If you have any more questions, feel free to ask.  :)