Custom icons for side menu

So I want a side menu on this site that is fixed or staiornary when you scroll. however id like to add custom icons on the side of them like in this picture. The cyan-ish circles that could be filled in when selected.

I guess my first question is how/whats the best way to add those and make them change when a new section is selected. In which the screen will auto scroll to that section.

The second question is. Is this layout that im doing the best way to add this? It seems like its working but i cant help but guess that there is probably a better way of doing it.

Here is my site Read-Only: