You can run up to three monitors including the internal, no matter the way they are connected. It's because the iMac 27 has two Thunderbolt ports but only one controller (in essence not giving it any advantage over the lower end models with regards to performance).
Ok, so they can all be used to extend the desktop? Or do they mirror one another?
I need to be able to play a video on one display, play keynote on the other, and then use the iMac itself as the desktop.