I think there are as many ways to set up your filing system as there are people doing genealogy. I'm going to detail just a couple.
1. The one I started out with used file folders, numbered documents, a master sheet, and family group sheets in a binder. This was a very awkward system that took up a lot of time to keep it current. I don't recommend it, but it is one that many people use.
2. Another method uses manila envelopes, one for each direct ancestor family, or in other words, John Doe's family envelope would include all the information you have on his children and their descendents except for your direct ancestor and their family would be in another envelope with all the children and their descendents except your direct ancestor. In these envelopes you keep not only the family group sheets for the married couple, but for their children that married except for your direct ancestor. Also in these envelopes you would keep the documents that deal directly with that family. You could end up with several envelopes with John Doe's name numbered 1-whatever. There is also the problem that sometimes you have information that should be in more than one envelope. When that happens put a page in the envelope that directs you to the envelope containing the document.
3. Another method requires 3 ring binders and page protectors. Everything goes in the binders except your research logs. Start with 4 binders and expand as the binders become over crowded.
I would look into other methods you can find on the internet and decide which one will work best for you. I am still deciding how I want to organize my stuff. I lost most of my documentation when we moved and I've got to go back and try to reconstruct it.
Dale L. Edwards