All the mods go to the folder "mods" that it's in your nexus tji main folder, in your case it probably is in:
"x:\...\Steam\SteamApps\Common\Nexus - The Jupiter Incident\"
Just extract the mod and put that folder in the mods one, so it ends up looking something like this:
"...\mods\STEC" and inside that folder there are a bunch of ones like universe, meshes, sound, music, textures, etc.
Then when you launch the skirmisher it should appear the STEC option.