Once you get involved in genealogy, you will find mountains of papers piling up on your desk. I am asked more questions on how to handle all of the information streaming in than on any other subject.
File folders are your best friend. You can devise any logical system that works for you. I have tons of file folders and they keep all of my loose papers nice and neat. I can find anything I need. I label my files with a black Sharpie which works just fine. Some people like to be a little fancier and use a label maker. Do whatever makes you happy. You can use regular file folders or the type that have the expandable bottoms. I use a combination of both.
A small filing cabinet will help you keep your file folders in order. I have one drawer in my file cabinet that contains all my folders labeled with surnames, another that has all of my active documents and another that has all of my reference materials.
The surname folders contain all of the hard copies of documents pertaining to each name such as birth certificates, death certificates, marriage certificates, social security applications, wills, land records etc. My direct line surnames have separate files for each of those categories. Some samples of active files are all my dilemma files (each file pertains to one brick wall I am working on), Possible Connection, Obituaries Not Entered (meaning not entered into my computer), Not Direct Line (collateral line information), Some of folders in my reference section are Marriage Abstracts, Will Abstracts, Cemetery Surveys etc. All of these are further subdivided by county such as Cemetery Surveys -- McDuffie Co, GA, Cemetery Surveys -- Columbia Co, GA.
Remember the 8 1/2 x 11 rule. All of the papers you file should be 8 1/2 in. x 11 in. It keeps everything nice and neat. Do not write notes on scraps of paper. Type them on standard sheets of paper. Print everything out on 8 1/2 x 11 sheets of paper.
If you have a document that is larger, and you can't shrink it down, you will need to fold the bottom flap up to have it conform to size.
Make sure every sheet of paper in your files is labeled completely and dated. If this information is not typed at the top of the document then you need to write it on the back of the paper. For example, if I have a copy of an obituary, it will be labeled "Augusta Chronicle, Wednesday, 16 Oct 1957, page 2, column 3."
You want to label it in such a way that if you ever needed to go back and find that piece of information again you would have no problems doing so. You would label it the same way as you document your sources which we have talked about before.
Keeping organized is a major battle but well worth the effort. If you are organized, you will have more time to do research, which is the fun part.