I assume that the question is just about Premiere Pro CS6, since the question is in the Premiere Pro forum. In that case, Harm's answer is correct.
But, if the question was also meant for other CS6 applications, then the answer is "yes". After Effects CS6 will use all of the CUDA cores in multiple cards, as long as the cards are of the same CUDA compute version. So, two Quadro 4000s would both be used. This is specific to the ray-traced 3D renderer, which is the only part of After Effects CS6 that is CUDA-accelerated.
Thanks for the follow up Todd, always appreciated. My feature request will follow.