I'm not sure I understand your question, but I can tell you what I know... so if you have an iframe you can just put allowtransparency="true" into the iframe tag. If you want to set one special color to transparency, you go to the stylesheets of the iframe: "filter: chroma (color=#XXXXXX)" with whatever color you want to have transparent. I'm not quite sure if that one really works, though... it's kinda not working with my browsers right now, but it used to, you'll just have to try it. If I'm not mistaken, other elements like tables and divs are usually transparent if you don't set a color.
I hope that could help you a little.
