Scrivener can look a bit daunting at first, but it’s not nearly as complicated as it looks! There are a few core concepts which it helps to know about right from the beginning and it’s useful to realise that NOBODY uses all the features of the program, so you definitely don’t need to understand everything at once.
My advice is strongly to do the interactive Tutorial first. It’ll only take an hour or two and it’s designed to help people in your position. By the end of it, you’ll have a good idea of why Scrivener works the way it does, and how to use it in the standard fashion for the most common tasks. You won’t need (or want) to use everything you learn immediately, if ever, but you’ll know the advanced features exist should you need them later.
Videos can be helpful, but you have to make sure they use the version of the software you’ve got, and they can’t cover the ground that the tutorial does. Much better to do the tutorial first, then look for videos that address specific issues you’re not sure of later.
As for your specific question, the usual method is to have a separate folder in the Binder for each Chapter and separate documents within each chapter for each scene, so that the Binder looks like an outline of your novel. You can move the chapters and scenes around in the binder (or outline or cork board) as many times as you like, while still being able to stitch together a virtual view (called a Scrivening) of the novel whenever you want – so for example you can look at all the scenes featuring the Hero’s Best Mate in one virtual document, even if they’re not next to each other in the binder.
If anything defines why Scrivener is such a useful tool, it’s this ability to cut your novel into smaller sections and manipulate them in isolation, whilst still being able to look at them in the combined view.
When you come to produce (“Compile”) the final document (for an ebook, pdf, word document etc), then you can add a prefix and number (Chapter 1…) and format chapters automatically, set headers and footers and so on.
But really – spend an hour or two on the tutorial first. It will save you many more times than that in avoiding wasted time and frustration.
HTH and don’t hesitate to ask questions as they come up.