Mengele and Eichmann would be tried separately. In some ways Mengele's trial would be even more horrific, given what he personally did especially to children. Eichmann was a grey bureaucrat simply doing a job efficiently (at least in his own mind). Mengele, on the other hand, was a fiend who with his own hands performed acts of horror on children. In the case of Eichmann, while the "following orders" defense is indefensible, he could legitimately say he was placed in charge of a program and endeavored to run it as efficiently as possible. See Hannah Ahrendt's "Eichmann in Jerusalem" and her discussion of the banality of evil. OTOH Mengele actively sought out his role, personally selected his victims (particularly twins), and either directly or by direct order caused unspeakable things to happen. He devised the "experimental protocols" which treated human beings as lab rats in the worst ways.