Okay, for anyone searching same question, I figured it out. As long as the 3 objects are not intersecting each other at any point, you can put all of them in a null as if they were 1 object, underneath the object they are being subtracted from. So, in this case:
Boole (A subtract B)
—Cloud(“A” object to be subtracted from)
——NULL (“B” objects being subtracted)
———Graph line 1(to be subtracted)
———Graph line 2 ”
———Graph line 3 “