I have made a flash client for my friend webpage to get .mp3's from an FTP server and play them through flash. I would like it to be able to be on the main page, and above the actual content like those really annoying flash pop-up ads. I assume that this is done with the Transparent, Windowless option in the Publishing Settings, but I have not been able to get this to work: it only displays like a normal flash movie. Can someone help me?

Your assumption is wrong those types of ads that can float transpartent ontop of the browser is using EYEBLASTER hosting technology. They can incorporate an invisible frame overtop the browser window displaying unique looking flash ads over HTML content. Enuff said. YOu won't be able to do this. Only way maby a popupwindow using dynamic html for borderless window popups... thats Ill I can think of.
my 2 cents