Yes, you could name the folders based on the users ID or username or other information stored in the users table (ID would probably be best since it will 1- be numeric and conform to web naming standards and, 2- always Unique). The ID will be stored in a session variable. In Digital File Pro, on the upload folder, you can click the lightning bolt icon and select the ID session variable.
If you wanted to use another column, you would first need to modify the login page.
Double click the Security Assist Authenticate user server behavior. On the Third step of the wizard, you can select database columns to store in session variables when the user logs in.