The plugin works by starting at some note, and then following the links to develop the hierarchy. That first note is the central note. By default, in the settings, it will look for CentralNote.md, however it can be any other file. In your case, where you use the Zettelkasten method (me too!), a good starting point would be to place the central note on one of your hub notes. This can be done very efficient by simply going to your hub note, press CMD+P, and write+select: “Map of Content: Set current note as Central Note”. If you then check out your tree, you will see your hub note as the central note, and then the hierarchy that is created based on how you linked your files.