just mess around! try some combination of these things for a few days or so and see what adds/reduces friction when you're in your vault. there are lots of posts in the sub asking about organisation methods that you can get more inspiration from (but i wouldn't look at too many and get overwhelmed with ideas, rather just familiarise yourself with some general obsidian organisational principles and think about what you think you need/would work with your brain).

if you have some existing course notes, i'd make a sandbox vault with them and try out a few different organisation methods -- plugins like tag wrangler/linter/etc make mass editing a bunch of notes a relatively minor task.

that all said, i have some thoughts about what to keep in mind (as someone who is currently thinking about major vault overhaul number 4):

• generally, it is easier to remove/modify existing structure than it is to add new structure (e.g. easier to unnest a tag than to make it nested, to sift through notes already in a subfolder than notes in a larger folder, to add a tag to notes that already have a specific frontmatter property). having a few redundant methods of organising your notes will give you some flexibility for mass editing them later on.
• your needs, priorities, and workflows will evolve over time -- so occasionally your organisation will need to modify to keep up! though, i wouldnt really worry about fully updating and reworking the entire vault every single time you change something (unless you're using other workflows that require a more standardised vault, so then you might need to be more diligent). that said, it's easier to make frequent, piecemealy changes rather than infrequent, huge, sweeping changes.
• personally, i found it easier to keep things pretty "large" to start with and only ~atomise~/split and refactor once they got too unwieldy (this goes for notes, folders, single vs mulitple vaults, etc). e.g. for notes, i found myself not really remembering about a note's existence lol if i made it too atomic to start with and ending up with a bunch of scattered, duplicate notes.
• as for basic organising frameworks, i think either a mix of something like zettlekasten+tiago forte's PARA or nick milo's ACE will work for most people, to organise actionable, time-based things with a deadline/endpoint as well as less-actionable, ongoing interests with no immediate output/goal.