All upper division undergraduate courses taken after graduating with your bachelors will be considered post-bacc. This includes taking upper div undergrad courses as a graduate student (according to our director of admissions). All graduate level courses taken during undergrad or graduate degree programs are counted in the graduate GPA.
Retaking courses that you got a D or F in is fine. However retaking a course because you got a C is probably not worthwhile. Adcoms will EXPECT you to get an A in a course that you retake...since you've taken it before. Therefore it does not say much in terms of how strong your foundation is in that subject area. It just says you can do better the second time. Thus, you should take advanced classes in the courses which you did poorly in. In regards to how they count retakes, AMCAS will count retakes as two seperate courses. Which means, if you took OChem twice. The first time you got a C, the second time you got an A, both will be counted on your GPA, rather than replaced by the most recent grade.