I’d like to do a major tear-up of my project, and I’d like to be able to go back to the way it was if it doesn’t work. Snapshots only seem to work for a scene, and when I tried to save my project in the scrivener folder with a new name I got an error message.
In other words, I want to snapshot the entire project and be able to roll back to that one if needed, without having to redo the entire set of folders from an upload. Any advice?
I’d suggest File->Back Up->Back Up To… It will prompt you with the default name of the backup (usually includes the original name plus the date, I think), but you can name it whatever you like. You can open that project backup and the original project at the same time to compare various aspects.
You could also duplicate the draft and or any other folders (Documents->Duplicate), but I think that’s a little tricky, as you can’t duplicate the Draft/manuscript folder itself.
… If you want to do this, then create a folder in your draft folder called “book” or “book 1” or whatever, drag all the other files and folders into it, and then duplicate that top-level folder and call it “book 1, draft 1” or whatever you like. The compile settings’ “Contents” pane will let you select “Book 1” as the draft target, treating it just like it was the main draft folder (so long as it’s a sub-folder of the draft folder).
Clear as mud? 
Try it on a “test” backup (File->Back up->Back up to…) of your project to get a feel for how this all works.
Or you can create a new, empty project, with whatever name you want. Then, with both the old and new projects open, drag everything you want to mess with into the new project from the old and tear away. The old project won’t be changed at all, and everything that is attached to a document transfers over. If you don’t like how you rearranged in the new project, just start over.
File > Back Up > Back Up To… is exactly for this. I’d suggest creating a zipped backup, both for the ease of copying it to other locations (such as an external drive) and because you won’t accidentally start editing it and destroy your milestone copy; you have to take the step first of extracting a copy of the project from the zip archive (you can read instructions for that here if you’re unfamiliar with the process).
Once you have the backup, then you can continue working in your current copy of the project to tear it to shreds and rebuild it into a new masterpiece. 
(For the record though, to answer the other question, you can use File > Save As to create a new copy of the project, but you cannot save into a .scriv folder. You should never save anything inside a project’s .scriv folder, as that whole folder and its contents make up the project and Scrivener needs to manage them closely. So if you did want to use Save As, just moving up a level in the file browser is probably all you need. I strongly encourage using the backup function rather than Save As for what you’re doing, though, because it won’t leave a trail of working projects on your machine that might be confusing later. Unless you’re planning to continue working in both versions of the project, it’s simpler to make the project backup, and then keep working in the original copy of the project so you only have that one active copy on your computer.)
Thanks for all your suggestions!
Hm,
Most of my projects evolved from a previous project.
Save as and giving it a name does a great job. Open the new project to verify it is intact and do a backup and all is well in your world of Scrivener.
Jim