Hello, I am new to scrivener. I opened the Novel Template, and I originally wished to make changes or edit directly the Standard Manuscript and Paperback Novel section since I really liked them, but then I discovered I am unable to because they are in PDF format. For this reason, I would like to find a way to match this formatting in the Text sections I create using Right Click → Add → New Text. Is there a way to do this? I would also like to know how to create Headers, Footnotes and such.
The best way to get going with Scrivener is to do the built-in interactive tutorial, found under Help. That will show you the basics and make it easier to understand where to find further info.
The standard format used in new documents is set in Preferences.
Headers and footers are set when you are done writing and ready to compile, and depend on output format.
Those PDF files are samples of what your work will look like once you compile the project to default settings. 
So you’re already set, if you use default settings for that template.
Otherwise, yes, it sounds like the tutorial is a good place to go for now. Footnotes and such are all covered there.