Painting with chocolate is much easier than you may first think. It is important to have runny chocolate to achieve a crisp finished piece. Start by painting the outermost color first (ie those colors you will see in the foreground) and work your way to the background colors.
For the iPad I started doing the most intricate parts of dark, white, and a mixed chocolate for the apps.
To layer colors without bleeding simply place the piece in the refrigerator between applications to harden the chocolate for painting over.
If you would like to use colors other than the shades created with chocolate and vanilla, I suggest using colored candy melts. Do not experiment with food coloring that is water based as this would cause the chocolate to seize up and harden. Food color gels may be used but requires some experimenting. I usually purchase multicolored candy melts and pick out the colors I need to melt.