@Glassbottom Hello and welcome
Hopefully I can help a little.
Basically, and this goes for most mods, you want to put the MEP folders you need into the Silent Hunter 3\MODS folder. No MEP folder needs to go within another MEP folder as JSGME sorts this out.
If you open any of the MEP folders or any other mod in MODS and see the folder "data", then you've installed it correctly. (With exceptions, always read the readme!)
So anyway, for MEP, I've followed the readme and activated these folders, with JSGME, in the following order:
M.E.P. v4.2
M.E.P. v4.2 to v.4.3
Optional - ShipVanishingHull for MEP v4.3
MEP v4.2 - VisualSensors for GWX3
The logic is: Mods further down the list overwrite the mods loaded before.
Hopefully this'll help get you going! Good hunting!