You could also use Tag Pilot for this which has a lot of different KML output and tagging capabilities.
Or you could do as Mr Pitman suggested. This function is out of scope for Map Pilot.
You could also do a free flight and use the log file KML that gets generated as a guideline for laying out your mapping flight.
Lots of options.
Any time you are travelling that far to map something it would certainly make sense to make sure you were well prepared with all the data you could possibly need before leaving a solid internet connection.
In Tag Pilot you can import multiple KMLs for a mission and Map Pilot 5.0 will have that capability. Or you could use Google Earth to merge the KML file features.
Again, lots of options.