I’m a complete newbie, so please excuse my ignorance. I have set up a Blank new project. It contains a Research folder. Under the Draft folder I have set up multiple chapter folders. I would like a Research folder under each of the individual chapter folders I have set up (as a subfolder). I tried duplicating the Research folder and then dragged the Research folder copy to my Chapter 1 folder. However, either I did something wrong or this structure is not possible as I was unable to drag pdf files to the Research folder copy (only the original Research folder will take a pdf) that I moved to the Chapter 1 folder. Can you clear up my confusion? Thanks.
Hi,
I’d definitely recommend going through the tutorial (choose “Interactive Tutorial” from the Help menu inside Scrivener), as understanding the Draft folder is important for working with Scrivener. Essentially, the Draft folder is special in that its contents will be compiled into a single text document during the “Compile” process - the point of Scrivener being that you can assemble your text in fragments in the Draft folder. Because of this special status, the Draft folder can only contain text files - you cannot drag PDF files, images files and such there (although you can drag images into the text itself, just not image files into the Draft folder as separate files). You can store such files everywhere else in the project - in the “Research” folder, or in other top-level folders you create - just not in the Draft folder.
Oh, and welcome aboard!
All the best,
Keith
Your Binder should look like this…
Draft
Chapter 1
Chapter 2
Chapter 3
Chapter 4
Chapter 5
Research
Chapter 1
Chapter 2
Chapter 3
Chapter 4
Chapter 5
Then, set up a 2-window view; Draft on Left, Research on right.
(Option-Click on the rectangle at the top far right of the Editor window)
Thank you!
…where by “should” Druid means “if you want.” 
Definitely a valid option to create the structure you describe, but don’t feel you can’t change things around as you get comfortable using Scrivener.
You can also check out Document References (Step 5d in the Tutorial) to link your draft chapters with the relevant research. By dragging the research document(s) to the Document Reference pane of each of your draft document, you can quickly access the research documents by clicking the reference links and opening them in the alternate split or a Quick Reference window (or even an external program).
So for instance if you’re working on a science fiction novel, you might want to organize your research into “Characters”, “Locales”, “Scientific Research”, etc. Then you could use the Document References to link the specific character sheet, location photo, and pdf on string theory to your Chapter Two draft document. If you want to take a look at all the character information for all your characters, it’s organized into a convenient group in the Binder, but you can still easily pick out what’s pertinent to a given scene in your novel.
Just one example. There are a ton of ways you could end up organizing and really finding what works for you and your specific project may take some playing around. I’m not trying to cause confusion, just demonstrate Scrivener’s versatility. 
Definitely run through the Tutorial project, though, as it will help a lot in getting you comfortable with the interface and some of Scrivener’s capabilities.
Welcome aboard!