Syncthing is very flexible, so there’s no single “correct” way of doing things. Some people may prefer having a few large folders and using ignore patterns to selectively sync their contents on different machines, others may prefer to have a large number of more specialised, smaller folders instead.
I’d suggest to give Syncthing a go first, just trying to make it fit into your workflow (instead of changing your whole existing folder structure to accommodate it to Syncthing instead). If this is your own setup, and not something used with other people, you can always make changes as you go further, if necessary.
Of course, I’d always recommend having a proper backup in place beforehand.