OK guys, this is the file that I use for my "invisible" sub:
http://files.filefront.com/NSS_Uboat.../fileinfo.html
Feel free to use it if it will help you. My method for hiding my sub in the navmap is replacing the "zoomed-in" version of the sub with this blank transparent file, and then change the settings on the nav-map configuration file so that it will show the "zoomed-in" icons in all but the farthest of zooms.
And yes, using waypoints does give away your position, so refrain from using them unless you are very close to land (in which case it doesn't matter if your position is given away, your navigation officer should be able to fix your position on the map very easily if within sight of land)