I have built notes with concepts, inspirations, and references for my story for a long time and have gotten a good bit of mileage out of the many Obsidian features for connecting them.
But in the end when I am trying to make decisions, I have the most success when I return to the vault and do a sweep for everything on or relevant to a specific subject and build a new note with those things embedded in it in a way that makes sense to me at the moment, as many things usually have changed since I originally created the notes.
If I know it is only a few pages and I am planning to get away from the computer, I may print and fill the margins and backsides with comments and sketches to be scanned and transcribed.
If they are longer and somewhat duplicitous, I create PDFs and either read them on my phone and do sketches and comments on paper, or turn PDFs to Photoshop files and chop them up and sketch/comment on using Cintiq. I should add that all of these things make their way back into my vault and inform my restructuring and further note creation, then the process repeats.
I understand that using paper is wasteful and can get out of control, but it can really ease my mind when I am free of computers. For example, I still like recording voice memos to actual tape, ha.
Thanks for asking.