Details depend on the exact driver you are using. If you go with the Unified Multi Touch Driver, you can (and have to) adjust everything in your adaptation layer, so you can use any I2C channel to communicate with the touch display.
All our finished drivers assume that the capacitive touch is connected to I2C1.
For your own application you can use any I2C instance, including the one which is used for the touch controller. However, be aware that the bus load on the I2C channel can be quite high if somebody moves his finger over the touch panel. Significant delays for the other application on the same I2C bus might be the consequence.
On the old library API, you need to provide a base address to use any other channel than I2C1. I recommend using the new API, but wait for the next release V2.1. In the current release V2.0 there is a bug regarding Mutexes.