Currently, I am using Larder (https://larder.io/), which is a bookmarking tool for developers. It supports categorizing and tagging bookmarks. Categorizing is done by folders. You can make a folder that has child. It will make you easier to organize bookmarks. Beside that, you can search your bookmarked links by tag, title, and URL.

This tool also supports synchronizing your GitHub stars. So, you can track updates from projects that you starred on GitHub. If you want to bookmark something automatically, Larder extension is available for browsers, Android, and API.

I have been using Evernote. I just clip a website or PDF that I want to read later. But, I don't know why I can't use it properly. Like what you said, the problem is me. I haven't used Pinboard before. It seems many people recommend it a lot.