I think you're not the only one who is getting a little bit confused!
With the patcher, you can fix the hydrophone, change the entries for real navigation in the menu.txt, and if wanted change the map colors. (Read the link to the post of TheDarkWraith in my last post,) The red colored items need to be doubleclicked to change them (enable them), and afterwards, just keep the patcher somewhere on your hard drive. No need to save it or to put it in your Silent Hunter directory or to put it in your Mods file. Just change the values in red and close the Patcher. Don't change any other things! TheDarkWraith made it easy to everyone by making this Patcher.
Maybe things become al itlle bit clearer, when you completely read this thread:
http://www.subsim.com/radioroom/show...?t=181433&page