Here is a video by THE Adrian Bowyer showing multi headed Mendel printing in three colors and challenges when CAD modelling it.
RepRapPro Multi-material Printing from Adrian Bowyer on Vimeo.
http://reprappro.com/Special_Blog?cmd=post&id=12
RepRapPro Multi-material Printing from Adrian Bowyer on Vimeo.
http://reprappro.com/Special_Blog?cmd=post&id=12