If the Uboats add-on is still on sale, you do need it. There are very few mods for v1.3, which is a crippled patch for a crippled v1.2, in my opinion. Why Steam does that I don't know. v1.3 does work, but not as well as it should.
When installing the game, do NOT put it in the "C:\ Program Files ..." directory. Use the Steam app and create a new Library folder that is NOT in that directory, such as C:\Ubisoft \ Silent Hunter... Otherwise, Windows will "protect" the game's files, and not allow a mod application to "stick".
Plotting your course is relatively easy. When on the navigation map, there's a little "line" tool, like third button from the left. After you click on that, hover over the Navigation map, and you should see a little "flag" icon with a line attached to it from your sub. Drag it where ever you want to place a waypoint, and left-click, which "plants" the mark, and sets you up to do it again. You can also select that tool, click and drag a flag to move a waypoint.
Off of the main listings, you'll find THEBERBSTER's
SH4 <> TUTORIALS <> HOW TO DO IT <... link, and in it is Rockin Robbins' links:
Sub Skipper's Bag of Tricks. The links on those pages are about the best way to explain manual targetting on a Fleet Boat. It's not like the Uboats.