I have found that many mods and tools that require files to be placed in the root Fallout 4 folder (where Fallout4.exe is located) are lacking installation instructions for mod managers. While these installation instructions still work, they can be difficult to follow. In my opinion using a mod manager to handle these installations has several advantages over manual installation.

This guide is specific for MO2. Check my Vortex guide for how to accomplish a similar installation method with Vortex.

Mod Organizer 2 cannot install mods that use the base game folders natively (where the Fallout4.exe, or Skyrim.exe are located for example). Luckily Kezyma has made a plugin called Root Builder that will enable MO2 to manage these applications.

Based on your settings, Root Builder will temporarily copy, or link mods that need to be in the base game folder. This makes it so that your game folder remains untouched and you have everything managed from one location, MO2.