Installing mods with Mod Organizer 2 from sources outside of NexusMods is actually really simple to do:

1. Open Mod Organizer 2.
2. Right click on any mod in the left pane.
   
3. Click “All Mods” then “Install mod above…”, or see the images below:
   
   
4. A File Explorer dialog window will open. Select the mod you wish to install. They will typically be distributed via archive files. (.zip, .rar, .7z)
5. A window will open. You can choose the name of the mod here.
6. You may be asked to replace an existing mod. If this is an update of the mod with the name you provided, choose replace. Otherwise, rename it to something unique.
7. The mod you added will now be listed in the left pane. Enable the mod by pressing the checkbox.
8. If the mod you installed includes .esp or .esm files, you can enable them in the right pane.

After following these steps, your mod should now be installed and enabled. Enjoy!