If you made a New Year's Resolution to get organized this year, here are few tips to get you started sorting through your mass of genealogy records. Remember that you should organize and document your research as you go.
Many prefer to color code their research. An easy way to do that is to assign each of your grandparents' families a color. For example, your paternal grandfather would be coded "red" and all of your research relating to his family line will be kept in red folders or folders with red labels. Keep all of your red files together and arrange them alphabetically by surname.
One of the simplest organization methods is to create a family group record for each married couple and then assign each family group to a file folder. The family group will be comprised of the married couple and their children. All of the family group's genealogical records created after the marriage will be kept in that folder. So the first document in the folder might be the couple's marriage certificate followed by the birth certificates of their children, family census sheets, etc. Note that the married couple's birth records should be kept in their parents' folders. You will also want to keep your research logs and notes in your family group folders. The FamilySearch Wiki has a really great description of of family group records and how to use them.
You can also organize your files by family name and record type. For instance, you might have folders for JONES: Birth, JONES: Census, JONES: Marriage, etc. Number each document included in the folder. At the front of each folder, create an index listing family members with the corresponding number(s) assigned to their document(s).
There is no right or wrong way to organize your research but, hopefully, this can get you started. As you get further along in your research you'll discover a system that works for you.