You don’t say what options you have used but most of the Delete Duplicates options work better if the songs have been identified by SongKong first using the Fix Songs task, and and finding album covers is also part of the Fix Songs task. So I would run Fix Songs over your whole collection, taking care of the options to decide if you want to correct existing metadata or only add metadata when missing, there are some predefined profiles that help with this.
Then after doing that run Delete Duplicates. By enabling the When find duplicates delete folder and any sub folders if empty or only contains the following files option you can delete folders that are now empty once duplicates removed.
We have a few videos but they are rather old
But the web tutorial is new and covers all aspects of SongKong