First I suggest you upgrade to the latest 9.1 version since 6.5.5 is very old.
Secondly, to take care of DBMS_OUTPUT calls you need the DbVisualizer Pro edition with support for this feature. If you don't have a license for DbVisualizer Pro, sign-up using v9.1 and in the Help->Evaluate Pro Edition.
Once DbVisualizer Pro 9.1 is running, there is a DBMS Output tab that will appear in the SQL Commander for your Oracle connection.
Hope this helps.