This is a very broad issue that can be split into more specific sub-issues.
When a new user opens the page, they're greeted with A LOT of text, and they have no idea what they're seeing in the visualization. If they want to properly use the tool, they'll have to read through all of the text (maybe multiple times) while using the tool, to slowly get a feel for what it is showing them.
It would be much better if the site took new users through a guided tour, where it would point to all the important bits and step-by-step explain what they do.
There should also be small tooltips for all buttons/settings, so that even a seasoned user can quickly figure out what a thing does, without having to read through the entire wall of text to find that specific detail. Tooltips could also be expanded to the nodes, connections and blocks that is shown in the visualization itself.
Some of the text should maybe be moved to a separate page or pages, to make it easier to navigate.