breaking in new pads and rotors (more complicated than the title states)

hi,
I just purchased some new Brembo Blanks and some new AEM HP brake pads for my 1990 Integra.
My current rotors are warped and my brake pads are unevenly worn (top is more worn than bottom & inside pad more worn than outside pad).
I have been reading about how you are supposed to break in rotors and pads separately, but I was wondering if I break in my rotors with my old pads, will this cause the rotors to warp (since the pads are slighly deformed, we're talkin about 1mm at most here).
I was thinking of maybe putting my new brake pads on my old warped rotors and breakin in the pads and then puttin on the new rotors and breaking in the rotors with the new (recently broken in) pads.

what are your thoughts on this?