I'm not quite sure what your getting at, but it sounds like your using one image as your Color image, another as the Alpha image. You shouldn't do that, they should all be one image.

If your trying to project an image you probably wont have to much luck, projections can be Ugly and take time to set up, and if you move your Object the texture doesn't follow.

I would use "Normal" as my option for 2D textures. Then it should map to your plane just fine. I just through a quick test together in Maya and it works fine.

So, make sure your Alphas are created correctly, and don't use a projection unless you have to.

Post back if it's still not working.