Ok, I've done some homework.
First there was no automated system on u-boats, everything had to be plotted by the Stauerman so probably getting a bit lost off course in bad weather was a normal thing.
I've found a great world map
Encarta which has superb quality, lots of names, even depths but most importantly precise longs/lats! After a while comparing places accordingly to SH3 map and prime meridian (blue) I've managed to make a photoshop template with long/lats for a specific SH3 zoom level. Take some time to see if it fits to the rest.
Below is an example of what kind of maps I'm thinking about. Precise maps of important areas with lots of geographical names to keep it more real/fun. You can photoprint them, store them on another PC? (I'm using an old laptop). With manual plotting you have enough time to compare different maps, think where to go and what to do next! Also you can put in your patrol log - "after going 5 hours at 284° we finally saw a tiny "Fair Island" on the horizon, a perfect place for an ambush".
Also my previous observation of Polaris confirms my position quite exactly. It was an hour before 00:00 (by that time there was 0 visibility) but the error should be small. Don't have a clue about longitudes yet... help!