I'd say simply add your logo layer, and reduce its layer opacity, but wither you have over complicated what you want t achieve, or I am not understanding you correctly.
It's the sort of thing you try for yourself, and come ask here if you have a problem. I don't think you will have, but if you do, upload a screen grab to help explain the problem.
I agree with Trevor. I think you are over thinking the issue. Just place a logo in the same document, scale it, adjust its opacity if necessary and your done. As for the background of the logo, that can depend on how it was created. Preferable in photoshop so that you have a transparent background. But if the background happens to be pure white or black, you can use blend modes to remove the background.
But I am getting ahead of my self. Lets see how you do, post your results, if necessary a screen capture of photoshop with the layers panel open.
ill post pictures tomorrow when I get the chance