I wanted to give an update to this. The Thuderbolt is still in demo at this time so I did get with my point of contact at Cisco. Their response is below but basically there will be features added as the device life goes on. Currently it does not work with multiple vlans.
"currently Thunderbolt discovers devices over the native VLAN, but we realize that discovery on multiple VLANs is necessary on many fronts, so we're planning for it in a future release. You could, however, manually add devices to your network, provided you know the device type, IP address and MAC address. All you need to do is mark the device which the added device is connected to, and click the '+' icon at the top of the topology. Fill in the details and the device will be created for you."
