For the most part, you'll be using them for the Challenge Tower full of touch based mini-games.
The latest trailer for 'Mortal Kombat' on the Vita gives us a look at some of the touchscreen controls that will be used in game. Before you get too worried, know that these controls aren't at all required to play the game normally, though the option is there.
The main focus of these touchscreen and Sixaxis controls is a Vita-centric Challenge Tower which puts you into iPhone game like scenarios. There's even a section that's essentially a 'Mortal Kombat' version of 'Fruit Ninja.'
The trailer also shows off the game in its traditional state, which runs at a nice crisp 60 frames per second and looks just as good as you'd expect a Vita version of the game to look.