If you are on a chromium based browser, I found these extensions to help dealing with large collections/hierarchies :

- Adding Faster to a specific folder with keyboard -> https://chrome.google.com/webstore/detail/faster-bookmark-ad...

- Tagging simply by adding #tag to the title. -> https://chrome.google.com/webstore/detail/bookmark-tags/edpe...

- Sorting/Searching using more powerful filters -> https://chrome.google.com/webstore/detail/bookmark-manager-p...

So instead of using a series of "_" folders, What I do is I append #tocheck to title, then I can also sort/filter them by date, folder, url...(and add other tags like #5stars, #ProjectC...)