For clarification:
The link Ducimus is giving you is for an application called JSGME (JoneSoft Generic Mod enabler). It is a stand-alone app, and the best method for enabling mods for SH4, or for just about any game out there. (hence the "Generic" part)
Download it. Read and follow the instructions. They're fairly simple, but for a beginner it may take some trial and error to get it to work. Took me about a week to get it to work, but that was a Vitsa thing. If you run into any problems, check the JSGME "sticky" thread at the top pf this forum. All the answers are there - just takes a bit of reading to sift them out.
Enabling mods "in port" means that you have to be at a point in the game in which you have completed a patrol. Enabling mods while actively on patrol is discoraged and can lead to problems. Always enable "in port". That said, the actual "enabling" portion is done outside of the game on your desktop using the JSGME applicaton - i.e. before you even start the game.
Good luck, and hope that helps. If you get totally lost, post your problem. There's plenty of knowledgable people around to help out.
Edit: looks like the JSGME user guide got moved to the SH5 Mods Forum here:
http://www.subsim.com/radioroom/showthread.php?t=163447
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