I mixed different colors of fondant with Americolor dye. P.S. Satin ice makes great premixed fondant colors if you need a lot of color and you don't want to wear out your arms mixing color. There's nothing like a fondant mixing arm workout.
The pizza sign on the top was accented with edible markers and the repeating Pizza written along the sides of the box was in buttercream. All the silver accents on the utensils were airbrushed with silver sheen.
When I've pained on cakes in the past, I have used watered down gel dye (which looks a bit like watercolor) or melted cocoa butter mixed with powder dye (which is heavier like oil paint, only less stinky).