It depends on the mod, but as Pisces said, the idea is to replicate the game's folder structure within the mod's.
For instance, in the case of the Underwater Visibility mod, you've to take its
environment folder and put it at the end of this path, like so:
Code:
\MODS\Underwater Visibility\ColdWaters_Data\StreamingAssets\override\environment
That includes JSGME's MODS folder and the mod's folder itself, which is up to you but determines its name in the utility's interface. Also, you might notice there's no
override folder within
StreamingAssets, but that's because the devs recommend creating it instead of overwriting stuff within the
default folder. I suppose it's a safety measure to preserve the original files.