From the launcher, go into Mods -> Mod Tools -> Create Mod to make the folder and info, then put your mod in that folder. After that, your mod should appear under "Mods" in the launcher.
Any mods you sub to in the workshop should appear automatically if they downloaded successfully.
I did that.
I created the mod myself, it does not show up in the launcher, though this could be to my own stupidity, as the mod itself (a name list) was formatted incorrectly anyways.