So I figured it out, testing a mod I'm working on to make the resource and crafting system more realistic.
Assuming you have a mod in mind, you first need to place the files in the game directory, 'mods' folder.
Run 'StorytellerNS' in the main directory, it should see the mod and open it.
Use the blue > to compile it.
THEN
You have to go back into the mods folder, copy all the files, and go to (this is the dumbest thing I've seen in game modding, I swear to God)
Documents\This War of Mine\Mods
and paste the files over.
Then the game should see them and let you activate them.