In the desktop app, I created a new folder called ‘Bookmarks’, then for subfolders I click the ‘+’ icon next to ‘folders’ then enter ‘Bookmarks/Whatever’ and hey presto, I have a new subfolder called ‘Whatever’ under the ‘Bookmarks’ folder. I then add tags in the ‘notes’ section of each individual entry for easy searching.
Benefits: free, open source, private, encrypted, syncs between devices automatically.