Mods folder works the same way it did on D:OS.
If you simply paste a package there without a meta.lsx, it'll overwrite the master files and *won't* show up in the mods menu.
If the package has a meta.lsx, it'll get a Mods entry. (you need this to add assets/globals/etc.)
https://dl.dropboxusercontent.com/u/32263228/dos/mods.jpg
