Ah.. ok... I misunderstood... Here's a step by step...
Assuming you installed JSGME to the root Silent Hunter directory and ran it once, there will be a directory called "MODS" under the Silent Hunter root directory. On my computer it looks like: (I renamed my Silent Hunter 4 directory to SH4)
D:\SH4\
\Data
\MODS
\Support
Ok, assuming you downloaded the three Trigger Maru files, open up the REL_Trigger_Maru_GFX_PAK_2_1.7z file with 7zip and there will be a file folder called REL_Trigger_maru_GFX_PAK_2_1 inside. Click and drag that folder into the MODS directory. Then do the same with the REL_Trigger_maru_1-6.7z and TMARU-Patch_1.6.3.7z files.
Now, start JSGME and you should see the three file folders on the left hand side. Install the GFX PAK first then theTrigger_maru then the patch file.
Do this same technique for any other mods you want to install. If you add a new file to the MODS folder while JSGME is running you'll have to quit and restart it so it'll re-read the directory.
And there you have it!
Cheers!