there are so many systems for document storage, have a look at hotscripts.com
I would not start to force one job to do another job just because both would use uploading functionality + database etc.
you will always have problems and it will never satisfy the needs really
for documents you will need a "dynamic web based filemanage" and that you will find at http://www.hotscripts.com/PHP/Scripts_and_Programs/Documents/index.html
for sure