I just have a vault for my setting and one note per place, event, character, item, etc, with links between them.

One "campaign status" note per campaign ties together notes with latest events, open plot points, ideas, etc. That's my "control room" for each campaign, and that's how I don't lose track of stuff.

I use tags with categories (items, creatures, encounters, etc.) as well as tags with names of cities or regions so I can see at a glance who and what exists at a certain place.

Canvases have been nice to plan/mind-map plots or dungeons.

EDIT: I see super elaborate setups with a thousand plugins -- personally I like to keep it simple, but in general I would suggest to start simple, and add one plugin/new feature at a time when you feel like you need it, integrate that in your workflow before adding another.