singedsun

I'm by no means a particularly sophisticated Scrivener user. So you might be doing all this already! But for longer pieces, each chapter gets its own folder, and each scene/set piece is a separate text file. I tend to write initial drafts long/in one piece. Then I chop the text into smaller pieces, because it makes it easier to rearrange the order, if necessary. As well as see what's missing (i.e., when it's not all in one file I don't get so caught up in the plot that I miss where additional details are needed for POV, character, worldbuilding, etc. I can really dig into a scene. The nice thing about Scrivener is that the files are so much more connected than in Word, so it's easier to edit this way.)

I use the notes file on the right hand side a lot. I feel like it's a good way to gently kill your darlings (they're not deleted! they're just sleeping over there where I can see them!) or to cannibalize text from my other works without dumping it straight in and dealing with detailed edits when it's not time for that. It's also a way to take research from the research folder and highlight it when the time comes.

I get rid of most of the templates. I use the research file to organize links by category (most common for me: time, place, occupational details). I research as I go, rather than do it up front, so that's helpful for me. I also have separate folders for images I find on Tumblr, as well as quotes from books that I'm reading.

I'm sure there are ways to link things together more as well, but I tend to keep a lot in my head, so don't bother.