Before you do anything, I would strongly recommend you obtain and read Dan Holme’s book published by Microsoft Press titled Windows Administration Productivity Solutions for IT Professionals. He covers, in detail, a very good solution for managing User Data and backs up his recommendations with strong reasoning.
You did not provide enough information because Windows Server 2003 R2 has better quota management then 2000/2003. When you read Dan’s book, it covers how and why to do quota and the dangers of having quota applies in the wrong way.
His book will help you understand and implement User Data and Settings