In this video we cover how to manually install Stellaris mods for the versions of Stellaris that use the new launcher
UPDATE: I forgot to mention in the video, but after you run the launcher, if you get some kind of error its okay, but you need to then run stellaris from the icon on your desktop or the exe where you downloaded it
Download Steam workshop files:
http://steamworkshop.download/
or
http://stellaris.smods.ru/