I believe you're asking.......How do you modify your game?
First off, make sure your using the latest patch for the game....which is version 1.5. Version 1.5 is the SH4 game that includes the "U-Boat Missions" (that adds the German side to the game). This version has the most/latest mods available for the game.
Without having the U-Boats added, the latest version is 1.4. There's still mods made compatible to v 1.4, but not as many as v1.5.
With a fresh install of the game (never adding a mod to it) now you're ready to add "JonesSoft Generic Mod Enabler" (JSGME) found
HERE. It's a good idea to follow the instructions found in the JSGME User Guide down loadable found
HERE. I can't express enough the importance of once adding JSGME to your "Silent Hunter Wolves of the Pacific" main game folder, that you open JSGME and find the menu heading entitled "Tasks..." and have the app "Take a Snapshot" of your clean game files. You'll use this "Snapshot" to verify your original game files are still intact, at a later date, after loading/unloading mods to your game. This is the best way of trouble shooting your game issues that will arise (and they will!!) after using mods.
Many mods are found in the "Downloads" menu section of
this forum page (look at the menu heading above). Their original [REL] (Release) thread can be found throughout these forum pages.
Choosing mods for your game is next. Always choose mods that are made specific to the version of the game your using (v1.4 or v1.5). Always confirm that when adding more than one mod to your game, that they are "compatible" to each other. If they don't say their compatible with each other, assume they are not. Adding them together to your game is at your own risk. This is where the "Snapshot" feature can help in telling whether your main game files have been corrupted or not, after adding incompatible mods together. JSGME will tell you when one mod changes another mods files when you "Activate" it. Sometimes this is expected, and perfectly fine, when a mod is "compatible" with another, Other times, this warning is letting you know there could be a conflict when playing the game with the mods you've chosen. Problems in not having a mod work as intended would be the least of the outcome....the worst being a CTD while playing the game.
Just keep in mind that the last mod added within JSGME will over ride a previous mod file of the same name. This shows the importance in mods over writing another mods files can still be OK....
IF the following mod is made to be "compatible" with the first mod. If it wasn't....use at your own risk.