Thunderbolt has nothing to do with your graphics card. They work independently. Thunderbolt is for fast data transfer to and from your pc to other devices.
See: http://en.wikipedia.org/wiki/Thunderbolt_(interface)
Apparently next gen Thunderbolt (40 GB/s) will use Display port connectors so you can move say 4K movies from device to device quickly (a lot quicker than USB3.0) but at the moment from what I've seen its primarily aimed at interfacing with external drives (that also have to have thunderbolt connectors) - 20GB/s (?)