First you find out what the highest mountain peak in the area is in feet. The automat needs to know this so it dont dive down into a mountain.
secondly you go into skyvector.com then you right-click on map, and choose "add gps" for each waypoint. dont add anything except GPS points
then you load up flightgear, go into route-manager, and load each GPX route you have made, and save it again as .fgfp. Save it in the default export folder, thats pretty much the only place you are allowed to save in.
then edit the files and add these 2 lines to each waypoint: