Using the website
The following features have been built in to the various html templates.
Finding notes
Use the Graph view, Backlinks, or Tags Page to find other notes, or just follow the links on the note that you're on.
If your notes are very neatly organised in a folder structure, then the Create Index from Directory Structure feature might also be something for you.
Header links
Hover over any header to see a chain link icon. Clicking on this will send you to the page and scroll to the header location.
Graph view
Read more Graph View.
Tabbing system
The default layout is documentation, which this site is built with. But for some people who are more into smart note taking, the Tabs Layout might be a better fit.