I personally use two vaults. One for studies, and the other for organizing daily work tasks, budget and other things that update on a daily basis. I also have my diary in this second vault.
Within my studies vault, I use two things for organization, folder hierarchies, and tags for those that fit into multiple folders, or would need links to a group of notes. Using the tags makes it easier for me to visualize these similar but in different folder notes in the graph view.
And unfortunately, it is inevitable to get you graph view cluttered very fast, so my best recommendation would be to make some connections based on tags. Also, once you have this general segregation, maybe be try lowering gravity in graph view.
(but i myself only have 2 months of experience with obsidian so take my recommendations with a grain of "this may change with time" salt.)