This thread will probably be moved to Help and Training.
First you need two miles of clearance between your waypoint path line and land, more if you try to set a waypoint next to a coastline. A waypoint path line can squeeze through between two points of land that are four miles apart. That will work in the center of the map, but not along the edges.
IF the original terrain builder is very precise, the map for setting your waypoints will still be off in the current version of the game for technical reasons.
In the center of the terrain map, everything should line up well, but the map is scaled for viewing and it's stretched along the edges by about two miles iirc. That's 4 pixels on a 512 x 512 terrain so take that into consideration as well. If you're working along the west edge of the map, the land mass will show two miles further west then it actually is.
Hope that helps.