If the mod has a 'Data' folder, open the Program Files/Ubisoft/Silent Hunter III folder and put the mod's 'Data' folder there. It will say it already has a 'Data' folder and do you want to overwrite the files contained there? Say 'Yes'. It won't change anything in the folder except files directly related to the mod.
Better still, get JScones's Jones Soft Generic Mod Enabler (JSGME). It lets you manipulate mods and remove any you don't like.
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