A very important part of genealogical research is organizing your information. It's best to create some sort of filing system right away, no matter how little information you have. Then you have a basis from which you can keep up your good habits. If you wait too long to start a filing system, what would have been a 15 minute filing project will soon become an all-day affair.
The two most important things to consider when filing your notes and finished forms are location and order:
Location. Wherever you decide to locate your notes (in binders, a filing cabinet, etc.) be sure they are easy to get to, orderly, and safe from damage. An old shoe box on the floor is probably not a good idea. Binders are nice, compact places to keep genealogical information because they're easy to transport to libraries or other places where you do your research. However, if you have stacks of information, you may want to use a filing cabinet to organize it all, and then just take individual file folders to the library with you, if necessary.
Order. You must decide in what order to file your notes. The most common way is to organize them alphabetically by surname with a folder or section for each individual. This folder will include any family group sheets that you've collected for a particular individual. You can also include any other documentation such as wills, photos, or certificates. For documents that you want to store somewhere else, insert a page into your files noting the name of that document, its content, and current location.
Genealogy Software. Of course, you'll also want to use genealogy software as an organization tool. It can help you put everyone neatly into their place on your family tree!