This is a great question. The "Writing" section of Notebook.ai will eventually include more organizational tools, especially those using/integrating Scenes. What I've personally been doing is @mentioning scenes in outline documents so I can move them around, reorder them, and write quick descriptions, but obviously I want to do tons more.
What's on the to-do list right now is a plot-based organizer that lets you import scenes (and whatever other worldbuilding pages you'd like) so you can organize them with any extra information you'd like. I'm planning on then tying that plot outline to documents, so you can either import your outline into a document and write it all or have separate documents for each scene.
It's a pretty hefty project and hasn't made it to priority #1 yet (although I've made a few prototypes to test small pieces of it) so I don't have any estimate for when it will be done, but it is something on my radar that I want to make.
I'd love to hear any and all feedback/suggestions you have on the idea, how you'd use it, what you like/dislike from other platforms, and so on if you've got the time (here's a form if you don't want to use the forums, too) – it's super helpful for me in planning/designing the feature. I originally built Notebook.ai to help myself prepare for NaNoWriMo (and originally just had it open next to Scrivener while I wrote) and I can write code that works well for me, but feedback and suggestions from everyone else has been invaluable in making sure new features are helpful to everyone and not just me. :)