I would simply have the completed bgl sent to the main FSSC folder then move it by hand to your CFS2 scenery folder.
or
use the great FSFlatten program on my site, easy to use, just move in a counter clockwise style, no limit to the amount of flatten points you put in.
It is a great utility, by Steve Greenwood.
Set your forward view to Hud, set your window view to top down. start fsflatten. name it "what ever". set the altitude you are looking for based on the lowest in your given area. Click new file, click new area, click add vertex at bottom. (Insure method at the top is set to area16.) Click your minus sign in the upper right to lower the program, hit P to unpause CFS2 , move your joystick ( plane ) to the next flatten point, bring up FSflatten, hit add vertex...minus sign again, p button again, move again...ect ect. Do not joint your final point with your stating point, FSflatten will do that for you.
Click create bgl. then exit. Go to the fsflatten folder locate your bgl and move it to your scenery folder.
Its like magic. I love that program.
Dave