It depends on what you want to mod, whether it be graphics or gameplay. Either way you can start by whipping over to the downloads tab and downloading S3D. It can do much more than I can. I use it for editing parameters: amount of explosive in a torpedo, how fast can it turn, how fast does it travel. With S3D you can alter the eyesight of pilots in enemy planes flying overhead, letting them see below the surface of the water, for instance.
Silent Hunter uses dds graphics. There are dds graphics plug-ins for photoshop, GIMP and other graphics programs, as well as stand-alone dds editors.
There's a lot more you can do but to do that you have to ask a real modder, not a wannabe like me.
