If I graduate from undergraduate college with a 3.3 GPA, but at a Post BAC program I have a 3.6 GPA, would medical schools my pre-med GPA as 3.6 or 3.3?
Medical schools will look at your overall GPA for all coursework you have taken prior to medical school. You have to submit all of your undergrad and grad school transcripts. Additionally, when you separate out science from non-science GPA, you will total in all courses you have taken - at least I believe that is the case. I took all of my college classes at one university, so I'm not 100% sure how it works if you take classes at more than one college. I'm guessing, though, that they would average them all in together.
Doc Admin is correct - everything gets averaged in together. And you have to enter EVERY SINGLE CLASS you have ever taken on-line, which is a lengthy and tiresome chore if you have attended a lot of institutions. Well worth it, of course, but still a pain in the bum.
The good news about this is that your post-bac work will most likely consist entirely of pre-med science courses. This means that the calculation of your science GPA will likely be higher than it would be if you had taken all of the pre-med stuff during undergrad, when your GPA was lower. (Obviously, then you wouldn't have needed to do the post-bac, right?)
Also, consider that many - if not most - schools will place a slightly higher premium on the most recent coursework you have taken. That is good news in your case!
Good luck...