There's five clauses in your selection, so if you're trying to identify all the parts, you need to do it five times:
[You] (subject); take (verb); knife(direct object)
[You] (subject); make (verb); incision (direct object)
No, 'profanation' is not the object of 'atone'. 'Atone' is intransitive.
But I'm not sure what you are trying to do. If you are attempting to parse sentences, I'd suggest you try with simple ones first.
Student or Learner