Yes, Yes, YES you have to put all your courses down, even retakes.
Remember that you are wanting to enter a field where honesty and integrity are highly valued!
If you are worried about your original grades on the classes you retook, take this into consideration: Atleast, you showed some persistence in going through the troubles to retake the courses. Many other applicants have had to retake courses. You just won't find too many admitting to this for fear of being flamed.
Good luck in the application process!
