Welcome to subsim!
I learned to plot/intercept/target using the excellent guide "Wazoo's Manual Plotting & Targeting Tutorial".
http://www.subsim.com/radioroom/showthread.php?t=206381
Its very well explained, and very effective (just ask the ships i come across LOL).
The link i provided is a copy of it here in subsim, the original one i learned from was on webarchive, but it doesnt seem to work anymore.
Also, now that you want to use manual targeting, i suggest you get rid of the mod you are using. I recommend Living Silent Hinter 3, its perfect for new players as its easier than vanilla, and it has the best looks sh3 can have.
You can also try vanilla if you want it a little harder.
Leter when you feel comfortable with targeting and other basic stuff, you can if you wish move to more difficult mods, like GWX, NYGM, etc.