Hi there!
The vision of the morality that can be found in Marlow’s Doctor Faustus is the idea of sin that Christianity defines as acts contrary to God’s will. By making a pact with Lucifer, Faust commits what we could consider the final sin. Besides disobeying God, he renounces his obedience, choosing to swear allegiance to the devil. However, in a Christian framework, Jesus Christ, the son of God, who, according to Christian belief, died on the cross for the sins of humanity, forgives everything.
In the "Discourse on Method", Descartes does not seek to teach people about sin and its consequences. Instead, he addresses how one can know the truth through science and the ability to think for oneself, including our five senses.
While Marlow's work deals with Faust's imperfections and God's judgment on those faults, Descartes simply recognizes that God exists, because of his own imperfections.
Hope this helps!