hey sean, I think you are referring to my post on the alpha trans.
Here is a good tut on ocaean waves by John Castarphan.
It may help you understand more of what I think you are asking.
http://vimeo.com/12972558
In it you will find- as I tried to say in other post.
The mixing of layers. In this tut it is mostly shaders,
You just substitute the shaders he is making with images per the image button. Then you can mix them as he does with the shaders.