Hello Sebbe and welcome to the forum!
every mod you want to install with the mod-enabler has to have the same folder structure than your SH3 Installation.
The root folder of the mod has to be the name of the mod and is free of choice.
If you have downloaded a mod that is jsgme compatible you´ll have to copy this folder the the MODS folder of jsgme.
After that the mod will be recognized by the programm, but only if the folder structure of the mod is done right by it´s author.
This is a typical folder structure for a jsgme compatible mod:
CA_dials/data/Menu/Gui/Layout/Dials1.tga
so you´d have to copy the folder "CA_dials" to the MODS folder of jsgme.
Another one:
TypeIId_skin/data/Submarine/NSS_Uboat2D/NSS_Uboat2D.dat
Copying the folder "TypeIId_skin" to the MODS folder would install this nice new typeIId skin.
Try browsing a little bit trough various mod folders and your SH3 installation, after a little time you´ll feel quite familar with the games folder scructure.
I hope i could help you a little bit, please excuse my english! :P
edit:
the first place to visit for sh3 mods