Hey Katie, I keep it real simple. I have a plastic file box that has four drawers. I keep purchased patterns in there. also if I cut something from a magazine I make an extra copy to store. I do not keep an index nor do I store patterns in any order. With all the free patterns available, and all the patterns in the two magazines, I rarely need to go looking in the file box!
If I get a pattern online, I just keep it in a file on my hard drive, and make an extra copy to store.
As far as the magazines, I keep the patterns in the magazine and store them in boxes in my shop, no index.