They way Mods typically work is this:
You put unzip the mod and then put the unzipped mod directory into the folder called MODS in your SH3 directory.
Then you need to run JSGME from the SH3 directory, and all your uninstalled mods appear on the left side of the screen. You select one of them, and then click the install button, and it installs and appears on the right-hand side of the screen.
As you install mods, if it conflicts with a previously-installed mod it will tell you. Sometimes it will work anyway, sometimes it breaks the previous mod.
I highly recommend GWX3.
Here are the mods I have:
Steve