Before you enter the Start Combat (or whatever it's called) command in the event editor, put in Change System BGM. It's on the first page of events, right column.
Then from the drop-down box, select Battle, and also from the other box, select the boss music.
Then insert another Change System BGM right after the start combat event command, and change it back to normal BGM.
Make sense? It's not that hard. :^^:
Um... this is also more of Troubleshooting. *moved*