To be honest, it's a very confusing process at first, since somethings don't seem logical.
It's important you follow the steps exactly:
1. You need 2 copies of your game (one is your main, and you do NOT have it configured to the update URL)
2. Once you make a copy of your entire game folder, Open the editor in the Copied Folder
3. Put the updater URL link in the copied folders Config.json. (You don't need to have any files uploaded to put the folder name in the URL) example: "https:/yourgamename.s3.amazonaws.com/update/update.json"
4. create a folder on your desktop called 'update'
5. Go to 'Tools' > 'Package Update' in the editor.
6. Select the folder of your Copied Game files
7. Select the folder you made called 'update'
8. It will package your update now.
9. Go to that 'update' folder and upload that directly to your Updater Host.
10. Success!
Important: Continue your work on your MAIN folder that is not connected to the update URL - if you config it to the auto-updater it will update itself to the previous version on your updater host.