It might be worth checking out this section in the manual, Martin. For GPS read FMC.
ADJUSTING FLIGHT PLANS FOR THE GPS
Please Note: This step is entirely optional Once you have created your flight plan a very useful feature is the Adjust FS FP for PF2000 option, available from the PFE main menu - but first a little more info so you understand why this can be so useful. When you create a flight plan in FS, or any other flight planner, it really doesn't care too much about the distance between waypoints or from your departure and destination airports, whereas ProFlight most certainly does. You see any waypoints that are too close together or too close to the airport can cause PFE a lot of problems when vectoring you from one to another. So during the compilation stage ProFlight will drop any waypoints it determines to be too close to either airport or too close together en-route. Consequently if you load the FS flight plan into the GPS it could and most probably will be very different (in terms of waypoints) to the one generated by ProFlight and used by PFE. What I like to do is have the two completely in sync so when I load the FS GPS I know it's showing me the exact same waypoints as there are in the actual ProFlight plan. And this is where the new option button comes in.