I don't know for sure if Smackdown is particular about it, but most 360 games I play with custom soundtracks are streamed straight from my iPod through a USB cable. The custom soundtracks are handled from the Xbox OS, which automatically overrides whatever software you have in the system.

Unless Smackdown has some kind of Playlist feature built into the game which might be what you're referring to. But the Xbox OS should override even that.