I'd take a look at Cricket (
http://www.soundcrack.net/cricket/index.html). It's not free ($150 though you might be able to arrange a school discount). It was written by a professional sound designer specifically for theater use. It can handle multiple outputs and fades between them, has a built in equalizer, play up to four tracks at once, and a lot of other goodies. You can also download it and try it for free, the only limitation is that you can't save your show files until you actually purchase it. I've ran entire shows off of an iBook and Cricket, it works really well and makes running cues brain-dead easy (press the space bar on each Go).