Installing mods with Mod Organizer 2 from NexusMods is pretty simple:

1. Go to a mod’s page on nexusmods, I’ve picked my own Mothership Zeta Rehaul.
2. Click the Files tab.
3. Click the Mod Manager Download button of the desired file. If there is only a manual download button, download it that way and move to this page: Manual MO2 Mods
   
4. Click Slow Download.
   
5. Mod Organizer 2 should automatically open. If not, open Mod Organizer 2.
   
6. Click on the Downloads tab on the right pane.
7. Double-click the mod that was just downloaded.
   
8. A window will open. You can choose the name of the mod here.
9. 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.
10. The mod you added will now be listed in the left pane. Enable the mod by pressing the checkbox.
11. 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!