Have you worked through the tutorial? You really need to. Scrivener is very weird (or more politely unique), so coming in thinking you understand how it works is a mistake.
Essentially, imagine you spent a full day outlining your book. You create 12 chapters with lots of topics under the chapters, and some points below those. - Sometimes you have sub-points, sometimes notes for examples. Now take that outline and make it your binder. Each chapter is a folder, each topic perhaps a subfolder or article then points or articles with examples beneath. The words on the pages are inside the article. Folders can be chapters.
Once you get it specific enough or have an idea that fits somewhere you begin writing your articles. You might have 12 folders, with 50 subfolders or topics with lots of articles beneath them. You can use the outline view to move things around or the corkboard to see everything beneath any parent point. When you decide the example you used in chapter three would work better in chapter 8, you move it.
You might add a preface folder and an epilogue or back folder and fill it with topics articles whatever.
You’ll stick research you aren’t sure where it will go (or are sure but will later prove wrong) and images etc. in the research folder.
You could have project notes, write notes to yourself regarding sections. You will move stuff around with the corkboard. It is all pretty cool, but there is no magic.
Hi, Steve, and welcome to the Scrivener forums! To answer your last question, users are able to create folders, etc., pretty much at will, for whatever their purposes may be. I would second steveshank that you work through the tutorial or glance over the manual to get a sense of how the interface works overall. It is, as steveshank said, unique, and greatly repays time spent studying up on it at first.
To answer the basic question: just create a new project from a template which does have the folders in them (i.e. one of the fiction templates perhaps), then open your existing project at the same time. You can then drag and drop the relevant folders from one to the other.
In more detail: most folders are just folders, but there are two or three which have specific capabilities. The main ones are Draft (or Manuscript as it is in some templates – it can be renamed, but it can’t be removed…), Research and Trash. You can also designate certain folders as ‘Template’ folders, where you can store templates for new documents which you use regularly: e.g. Character Sheets in novels.
But all this is fairly advanced stuff – before you do anything else, the best advice anyone can give you is to follow the other posters here and do the Interactive Tutorial. For the sake of an hour or two going through this, you’ll get an understanding of how everything is supposed to hang together – you will be able to use Scrivener far more effectively far quicker than if you try to muddle through.