Hello, this is actually pretty easy. My setup is following:
Apple Thunderbolt Display
MSI N680GTX Lightning
Intel Core i5-3570K
MSI Z77A-GD80
Important thing to make this work is to have motherboard with thunderbolt port and support of LucidLogix Virtu MVP (which P8Z77-V PRO/THUNDERBOLT has) and processor with integrated graphics.
If you don't have other monitor that you can plug in directly to discrete card, you will have to remove the card first (otherwise you won't see anything at all).
1) go to bios setup and find Virtu Technology configuration (for me it was under Advanced -> Integrated Graphics Configuration)
2) enable Virtu Technology and IGD Multi-Monitor
Now you should be able to startup computer with only Thunderbolt Display connected and actually see stuff, however it won't use discrete card yet.
3) install latest Virtu MVP driver (http://www.lucidlogix.com/driverdownloads-mvp.shtml - or directly from your vendor) and define which programs should use discrete card
And now you are set. Your system now should use integrated card except when you are using one of the programs you just defined in MVP Control Panel - in that case Virtu MVP will somehow reroute output from your discrete card to the thunderbolt output. It actually doesn't affect performance negatively and can even boost it if you enable Hyperformance. I don't think it's possible to use ONLY discrete card for everything and still redirect it's output to thunderbolt - if you find out how to do that, please let me know