Notes has seen some serious tweaks in Mac OS X El Capitan, but it doesn't take full advantage of the new tagging feature.
With the tags feature, you can tag a file from the Save dialog, the Finder, or the iCloud Library. When you click in the Tags field, you can choose from your recent tags or type in a new one.
You can create Favorite tags that are always accessible from the contextual menu, making it easy to quickly tag a file. Files can have multiple tags, giving you the flexibility to organize files across multiple projects. Your tags automatically appear in the Finder sidebar, so it’s easy to find tagged files no matter where they’re located.
This is very handy — and you can tag notes in the Notes app. However, there's no ability to tag individual notes in the program. That would be even handier.