The Source Documents column usually lists all documents found in the Source Documents folder(s), mainly because the decision who will get access to which document will only be taken later on when QDS publishes User Documents. YMMV.
The User Documents column lists documents to which the selected user/group has been granted access. How do you grant access to documents? There are a few methods. The most important ones are:
Explicitly by listing users/groups in de Authorization tab in Documents->User Documents. You do not need a Publisher task to achieve this. Note that your QVS must be an Enterprise Edition server, and security must be set to DMS. Otherwise this tab will not be available.
By way of Publisher tasks. In the Distribute tab of each task, set the method of distribution and the users to which this document will be available.