I would have a different folder for each subject, personally. Plus the following: (this is advice I posted in a past thread about the same topic)
Get yourself a ring binder and some file dividers. Date your work. Organise your notes into separate file dividers for separate topics. That way, when it comes to revision time, it'll be a lot easier and a lot less confusing!
I keep my worksheets in chronological order with my written notes. Then, in my revision time, I use notes, worksheets, text books, revision guides and websites to compile the perfect set of notes for me!
Those notes are marked in red pen at the top of the page with the subject and module title. Once the exam is finished, they are filed away, one module in one polypocket, and then in turn organised into a box file just in case I need them for future reference.
Remember to recycle anything you don't need anymore too.