Hi! I started from pre-existing, different vaults for different activities but in the end, I converged to one vault for everything.
You could define vault as you want, recursively every folder in the root of the vault and will appear in the vault, for example, I have a structure like that
So you could nest as much as you want, but think which way it will be the most convenient for you!
Obsidian will see all markdown files, after creating the vault you could still access the files as before, Obsidian will only create its own config files (hidden) in the root of the vault
If you also use other markdown editors to edit the files the only thing you need to think about is that some of them [editors] don’t follow [[ ]] links if linked file will be in another folder (for example 1Writer on iOS)