CPSelect rotates and scales correctly, but does not translate the second image correctly on top of the other.

I am currently working on a script which overlays one image on top of another based on three fiducial markers that are present on both images. The top image which is being transformed is a binary image which the background image is color. I can correctly get CPSelect to rotate and scale the top layer so that it matches the background, however I'm not sure how to translate the top image so that it automatically matches up with the bottom image. Also, since the top image is black and white, I would like the white to be transparent so that only the black portion is superimposed onto the background. Any help would be greatly appreciated. Thanks!