Your objective should be to come up with a logical system of storage. It doesn't matter if the system seams haphazard and makes no sense to anyone but you. As long as it serves its purpose of helping you find information quickly and easily, it's a good system. If you know that you keep all of the census data at the very bottom of the heap, it will be rather easy to find a particular census record. If you keep all of your interview notes just above the marriage data in the heap, it is a simple task to find that interview session you had with Uncle Charlie on March 3,1990, assuming you have your papers labelled.
Papers are less likely to get lost if they are in small files.
Be consistant in your labeling and storage methods. For instance, place the name of your interviewee in the upper right-hand corner of each page and it will be easy to flip through the papers and find your notes on the interview with Uncle Charlie. Or put the name in the upper left-hand corner, or at the bottom right, whichever is easiest for you. What is necessary is consistancy. If you do certain tasks the same way every time, not only you, but others will be able to find data quickly.