I figured out how to get the mods manually.
seems that steam downloads them, but doesnt put them in the right place at all.
I looked for new files and saw the mods I wanted with the civbemod extension. I expanded them using 7zip into a folder with the exact name of the mod, case counts I think.
Then I moved those expanded folders to Documents\My Games\Sid Meier's Civilization Beyond Earth\MODS]
Now the mods show up, but strange that they wont update and they will never get there by themselves.