Observer's Assisted Plotting Mod will remove all ships from the nav and attack maps. If you run the cursor over the ships you will see a dotted circle. If you click on a circle it will say "Unknown". If you lock onto a target and ID it yourself or have the Weapons Officer do it, it will then show up on the Attack Map. Once you enter info on it that will also appear, as well as on the Nav map if you click on that particular circle.
I love this mod, even though I don't play at 100%.
http://www.bts-mods.com/?page=sh3user=sailorsteve
As for course plotting, I can't help you there. Sorry.