Thanks in advance,
First pile is everything you write in the story. Aka the actual novel.
Second pile is everything about what you write. Aka research and references.
Then you go and fill the piles with a rough outline. Keep a clear goal in mind when you do this. How do you want your story to release? A traditional book profits from using the chapter/scene approach that Scrivener uses by default. Webnovels on the other hand could perhaps use an Arc/Release approach instead? Up to you - it's just something you should figure out before you start.
Likewise, how do you want to granulate your references and research? Do you keep a character sheet for each character? Maybe you make smaller piles for major and minor characters? Do you need a pile for locations and another for key items? As you work this out, you'll slowly create a tree structure that will inform how you work in the future. This is why it's important to take the time to do this right. If you ignore this, you might as well not use Scrivener.
Once you're got a good outline for your workflow going, you start by setting it up in Scrivener. Use the piles as your folders and then make templates for everything you need. Character sheets? Template. Locations? Template. Items? Template. Keep these in the template folder. Now that you've done this, you can start to fill it with content. In your case, I suggest going through your 8 notebooks and copy pasting information into the respective folder. This is the painful part. This is why you're out of luck, because the software can't sort it for you - just make it easier to keep it sorted.
After you're done with that, you're good to go. You can then make full use of the features it has. Use word counts to balance out your releases, maybe sort it by number of drafts - edit keywords you can follow up on and keep a sheet of notes what you should do. Set dead lines and targets, mark content for rework... yeah it's all there. But to get there, you need to organize your project first. Scrivener comes with a few suggestions but I've seen these do more harm than good - because each Author has their own workflow.
You can seperate Scrivener into three parts:
Binder. A sorting system you need to setup to better organize your writing.
Writer. Software to help with formatting and publication.
Tools. Added functionality such as statistics, keywords and word counts.
When you learn to work with the software, you really need to understand Binders first. They're THE raison d'être for the software. Thankfully, they're very similar to folders in windows or every other tree structure. With that in place, you can really ignore most other functions and just get to the writing. Learning by doing, take it one step at a time and when you think of a neat function you could use, chances are Scrivener has got it. You really don't need to know all it can do. As for publication, keep one acronym in mind: KISS. "Keep it simple stupid". The less special formating and fancy stuff you use, the easier it will be to publish.