The only way I can think of placing navmap marks using custom descriptions is by hand placing them in-game and editing the "Mark X"-text in a .map savegame file out-of-game and reload. I think this is how SH3Gen does it.
Take a look at an excerpt of one of my .map files below (it's in your MyDocuments\SH3\data\cfg\Careers\*player_name*\*pa trol_number* folder) You'll see alot of marks that SH3Gen added based on the intelligence it has. So it does write to your savegame files, but maybe not critical files. Atleast, I don't know what happens when you screw up the syntax. Will they be ignored?, or cause CTD? Don't know) Ruler, range, angle and waypoint sections are further down the file. However it seems to miss important information like circle radius or endpoint of the ruler. So they must also be stored in some other savegame file.
Code:
[Mark]
PointsNb=428
Pt0=-8633782,4342699,0,-Convoy-
Pt1=-10432753,3458574,0,-Convoy-
Pt2=-8546785,1983000,0,-Convoy-
Pt3=-9723398,1771374,0,-Convoy-
Pt4=783002,7719000,0,-Convoy-
Pt5=4017525,8312201,0,-Destroyer-
Pt6=4021550,8422661,0,-Destroyer-
Pt7=4808148,7784480,0,-Destroyer-
Pt8=5025748,8337093,0,-Destroyer-
Pt9=2220391,8328901,0,+DD Leberecht Maas+
Pt10=2217651,8329111,0,+DD Paul Jacobi+
Pt11=2217621,8327671,0,+DD Bruno Heineman+
...
According to the Sh3Gen readme quoted above by Irish1958 the text must be within 19 characters, so it has it's limits. (didn't know that before) And it's cumbersome doing a save-edit-reload all the time. But alot better than making messy hieroglyphics with the line-tool, IMHO. As the little endpoint crosses and length numbers are plotted also (and sometimes the lines are not shown based on line-length and zoom-out level, making it even less clear)
I'm afraid there will not be an in-game solution (ever) since the game is too old. The irony in all this is that Dangerous Waters/Subcommand could not draw lines (except in the mission-editor!!!) but did place editable marks and circles (and also had a temporary range/bearing tool) during playing, while SH3(/4?) cannot edit those marks in-game yet has all those other neat kind of drawing tools. This is really weird.