I heavily use properties to make things related to each other. You can use wikilinks in properties, so you can keep the main text clean of links and all this stuff.
For example I have a scene note where I write the actual scene text. It has a property “Story” linking to the main note with the whole book overview. It also has a “Characters” property with links to notes about characters, involved in the scene. And the “Notes” property with links to any additional notes related to the scene. Characters and notes are also linked to the story, so everything is connected. You can create any additional properties like that, for example “Places” or “Storyline”, depending on your needs. I have special templates for my writing, so I don’t have to add all this properties manually.
When I am plotting I also create a lot of additional notes with ideas, worldbuildings pieces, characters traits and all the random things. I try to keep them atomic and connect Zettelcasten-style, because it works very well for the thinking process. It is good practice to connect ideas to the scenes, so you immediately see how they work in the plot.
For example recently I thought about one of my characters and it occurred to me that she tend to avoid direct confrontation. So I made a note about this. Then I added a list of all the scenes where it happens. Then I added a link to a note about her backstory, because I think this trait must be somehow related to her past. Then I started to think: okay, but is this a character’s flaw? Does it affect the plot? Should I add more scenes where she overcomes this? Etc, this way of taking notes really makes my gears turn.