You can drag nodes around to reorganize them, and connected nodes will follow them. Just tinker around a bit until you find the structure that suits you!
However, if you reopen graph view, the structure is reset, so you may want to keep your graph view open at all times, by pinning it.
And for the note-taking approach, the graph is supposed to represent the connections between topics. I usually have a table of contents note connecting to all other notes of that topic, and in the case of mathematical proofs, I usually link notes that my proof uses.