Sorry if this is too late, but yes, that is what the alpha channels do for you... (most of the time)
A poor workaround for your situation might be to make your own "alpha" in photoshop, and use that as a track matte for your fireball layer. ? maybe... not sure...
Next time, try rendering everything together, only use the "Background" shader on all of your "outer" particles or geometry, that way, your fireball alpha will make your fireball look as though it were inside....
Sorry if I sound so vague
Israel "Izzy" Long
Motion and Title Design for Broadcast-Film-DS