Peter's solution inspired me to a (to my mind, at least) simpler solution. Now suppose it were not possible to arrange the cubes to produce an equal number of red and blue faces on the large cube and assume (this probably doesn't need assuming but we can assume it wlog so let's just do that) that there is a configuration of the small cubes which has fewer than 12 red faces on the exterior of the large cube. (As in Peter's solution, a configuration of the smaller cubes consists of a choice of a vertex from each of the cubes.) Now consider a configuration of the small cubes which has as many red faces on the exterior of the large cube as possible without having more than 12 (exactly 12 is, by assumption, impossible). If any of the vertices in the configuration were not a vertex on that cube with the maximum number of incident red faces then by following a path from the chosen vertex to a maximum vertex (each step only changing the number of red faces on the large cube by 1), we would at some point increase the number of red faces on the large cube by 1 which is, by assumption, impossible. But if our configuration consists only of vertices with maximum number of incident red faces then the exterior of the large cube must have at least half the the total number of red faces, contradicting the fact that it has less than 12.