I think VMS Bundle can not configure several VPN3000 remotely . It only does monitoring. Here are Q&A regarding VMS Bundle:
Q. What is CiscoWorks2000 VMS?
A. CiscoWorks2000 VMS is a management solution bundle that provides Web-based applications for monitoring and troubleshooting enterprise Virtual Private Networks (VPNs). It also provides features for configuring and monitoring firewall security.