Syncing between Aeon Timeline 3 and Scrivener can work with either app as the starting point and at anytime during the creative process in either project.

Start with an Aeon Timeline project and sync to Scrivener, or if you already have a Scrivener Project in progress you can use the sync function to create a new Timeline – which is great if you have 1 book and are not planning to make it a series with a story arc you want to maintain across all books.  Syncing each book into Aeon Timeline 3 can give you an over arching view of your novels.

Just a few thoughts there to get you going.

Are you using Aeon Timeline to sync with Scrivener, or  maybe to Ulysses (look at for the video on this shortly). Let me know in the comments.