Mod Organizer not Installing Mods

[RadioactiveSoup]

Okay, so recently I've reinstalled Skyrim and decided to import all the mod from Nexus Mod Manager to Mod Organizer while I was at it. But when I installed all the mods and loaded my previous save, it didn't have all the mods showing, via animations/armor/weapons/etc. Basically I was naked and in T-pose. Then I check my Skyrim folder and realized that all the data from the mods were not installed in the data folder. Is it possible I didn't set up Mod Organizer correctly? Or am I just stupid? ._.

[EssArrBee]

Mod organizer doesn't install in the data directory. It uses a virtual folder so you don't have to clutter up your SKyrim install.

[DoubleYou]

Launch Skyrim through MO.

[RadioactiveSoup]

Just figured this out with the help of my brother. Sucks I can't directly access through the desktop though. :c Thanks anyway guys!