Yeah I use the waypoints(navigator ensign I guess) when I enter combat and once I reach my objective and start searching out targets. But for the way to and back from objectives I like to use manual navigation, gives me something to do other then turn on high time compression and watch my boat warp across the map. One thing I have noticed, and I'm not sure if it's my periscope mod or what but, the periscope bearing markers are off a tiny bit. I'm thinking .5 degrees or something small like that, but the game rounds up/down so sometimes I end up heading way off track even over the period of only an hour, it's sort of annoying but I guess it could replicate the problems with wind and current while navigating on the open seas.
Here's something I made up for myself that you will probably find usefull, it's a nomograph and a conversion chart that I have printed off and it saves me a lot of time as apposed to draging out the gramophone which in TM is modded to be a conversion chart. I'm not sure if MS Word will open it because I saved it in open office but you can try anyways(or download open office):
http://files.filefront.com/conversio.../fileinfo.html