In Marlow's Doctor Faustus view of morality, there is the idea of sin, which Christianity defines as acts contrary to the will of God. In making a pact with Lucifer, Faustus commits what is in a sense the ultimate sin: not only does he disobey God, but he consciously and even eagerly renounces obedience to him, choosing instead to swear allegiance to the devil.
In a "Discourse on Method", Descartes does not seek to teach people of sin and its consequences. Rather, the author simply addresses the manner in which one can know truth through science and one's ability to think for themselves apart from our five senses. He believes that God exists because he can reason that there must be a mind which knows perfection and he understands that that he, himself, is imperfect.
Marlow’s work is about the imperfections of Faustus and God’s judgment on those faults, whereas Descartes simply sees the fact that God exits, due to his own imperfections. His thoughts go like this, "If I am imperfect and can consider that there is such a thing as perfection, then there must be a God who is perfect."