You really cannot do much with a 6509 (VSS or otherwise) from CNA. Note the specifc answer to your question is covered in the Release Notes:
Note 
The Topology View of Network Assistant supports Catalyst 6500 switches. You cannot add these devices to a community or cluster, but you can start device manager for them from the Topology view.
Cisco really steers you to their enterprise class network management products (e.g., Cisco Prime LMS) for the 6500 product line.
Hope this helps.
