I'm making a Minecraft character and for the face I made holes with the boolean modifier; inside the head everything is grey but I want to have the colors of the front side of the head. I want to be able to modify the cubes which cut the holes so I don't want to apply the modifier.
The Boolean mod will place whatever materials are on the mesh used to modify the object provided that they are also included in the modified object (i.e. the big cube). Only colors that are in the big cube will be received from the modifying mesh (the little cube). You can see a dark green on the underside of the little cube but it is not applied to the cavity because the big cube does not contain that material.
So you must make your modifier mesh cube exactly the way you want your colors to appear in the head cavities.