That's right, your sub icon no longer appears on the map (transparent .tga file) when using manual navigation.

What I realized when doing manual navigation is that is was easier for me to sail from Willyshaven up close to Norway and then west to the Atlantic above the Shetlands. I no longer wanted to chance going between the Orkneys and Shetlands since you never know when the weather will turn bad and you no longer have a good fix. Then I picked up "Iron Coffins" again by Werner and it had a map on the inside front cover showing the same exact sub path used during WW2. It was a neat revelation that corresponded to my in-game experience.

One other really nice immersion factor I should mention is that I now just configure manual targeting from the TDC in the conning tower. It feels more realistic to turn those dials on the 3D screen instead of using the 2D notepad from the periscope screen. The downside is when the weather is rough the conning tower really rolls with the waves!.

Nice bump in realism for me was picking up a circular sliderule at an antique shop and using that for targetting. It's really very easy, actually - just get two bearing + range readings, and you've got AOB and speed from the sliderule!

RE: not using the 'lock' capability...unfortunately, that's the only way to get the range from the stadimeter, and they DID have that in WW2. I rationalize this as simulating the captain just keeping the scope on the target to have the range read back. I don't use it for the speed calc as - see above - sliderule handles that.

RE: 'manual navigation'. Sounds great, but it also sounds like something another officer on the crew would handle, no? I rely on waypoints to cover the LONG travel times, as having the manually navigate the Kiel canal....*shudders*....

I must admit for the Kaiser Wilhelm Kanal I use the auto plotting mod and sometimes also use the waypoint system (like for crossing the atlantic high speed to the US coast) But the rest of the time I like to do it manual, keeps me busy in bad weather (and because I like it as I have been navigator on racing sailboats for many years..:D)