Mod Organizer Not Installing Mods

[smittttty]

I'm having a problem where Mod Organizer isn't actually installing my mods.

Whenever I download a mod and install it with Mod Organizer, the mod seemingly installs with no errors. When I start Skyrim the mod is installed and works fine. But when I actually navigate to the Skyrim install directory, then into the data folder, none of my mods .esp's are present. I am sure that I have the correct directory set in Mod Organizer. This is problematic because if I run an external program like LOOT or WyreBash they don't detect my Mod Organizer installed mods, because the mods aren't actually in the data folder. Only by launching the game through Mod Organizer do the mods load, if I use the skse launcher inside my Skyrim folder, or just the default Skyrim launcher, none of my mods installed by Mod Organizer load. It's like Mod Organizer is injecting the mods into the games on launch. If I manually install a mod by dropping the files into the data folder, it will load up no matter how I start the game.

Anybody have a solution?

[KingLuxion]

To use LOOT and Wrye Bash in Mod Organizer, you have to set it as an executable using the gear icon on the top menu. The reason there isn't anything in the Skyrim install directory is because Mod Organizer makes it to where you can use mods in your game and leave the install directory alone. So if you mess up when you're modding, you don't have to completely reinstall Skyrim.