If you ARE new to genealogy, it is important to realize that there is no right or wrong way in order to organize your digital and paper genealogy files. Everyone does so a little (or a lot) differently and it really comes down to a matter of preferences, as long as your style is functional to you.
Between my and my husband's families, I have around 20 different binders in which I store paper copies of most of the documents I find. They are organized by surname; some of my binders contain information only on one surname, others contain more than one surname. I label all of the binders on the front with a simple cover page.