I got Mods running today - GOG installation of JA3.
Download the mods from Nexus Mods
Go to "%AppData%\Roaming\Jagged Alliance 3"
Create the Mods folder (I used that exact spelling/capitalisation)
Expand the mods into the new mods folder
Make sure you start the game fresh
Enable the mods in the in-game mod manager
You'll probably have to start a new game, mods I tried didn't work with an existing game/save file