It's been awhile but im pretty sure you have to shoot the four buttons which surround the female boss (the ones which have trails of red liquid leading to them).
That should bring out the male boss on top. Keep shooting him until he's dead. Once that's done, that should make the female vulnerable so then you should be able to kill her.
[Edited by kiph, 11/24/2007 3:04:12 PM]
that is correct in what you have said once you shoot the four type cogg looking things then the blood stops coming down and she/she is the vunrable to be shot at