This is my opinion, but doesn't the Javascript version of always on top work just for that window? If you have explorer 7, a new tab will cover up the popup. Not sure about firefox. You will also have the warning about popups and axtiveX show up. I suggest using loadmovieNum as that is what I did for my own site. You can navigate my site and the mp3 player is always there. And it would be easy to have a button that plays only my mp3 player.
But making an mp3 player in koolmoves is very easy and there are apps here that can make it even more simpler.
Hope this helps.