I am the parent of an applicant. This is my daughter's second year applying, and from our experience I can tell you that Anatomy and Physiology are VERY important to PT schools as is your entire pre-req GPA. My daughter received a B in Anatomy and a C- in Physiology (her school broke up A & P into 2 separate courses), so she repeated Phys her senior year and received an A-. She also repeated Physics II after graduating... she got a C+ the first time and an A the second time. She applied to 12 schools this year, and even with the repeated grades and working full time as a PT Tech, she was accepted to NONE so far (interviewed and waitlisted at several). Repeating the courses brought up her pre-req GPA from 3 to 3.2 because PTCAS averages ALL the grades and the C- lowered it significantly (it's a 3.4 if you only include the higher grades and her overall GPA is 3.4, 3.45 w/o lower grades). Also, she had a legit excuse for the lower grades... she received both of the lower grades in the same semester when she had a family crisis which played out over a couple months, so she missed a couple classes and was very distracted. She explained this in her application and on interviews, but it didn't matter. They want high GPA's and/or high GRE's. That's what it comes down to, so take every pre-req grade very seriously because it weighs a lot in the admission process. Also, if you ask any current PT student or graduate for advice, one consistent thing they'll tell you is "KNOW YOUR ANATOMY" before entering PT school. Undergrad Anatomy is NOT easy and it won't get any easier in PT school, so don't take it lightly and be prepared to explain your D in your application and at interviews. I don't think it's worth explaining your logic about not taking the exam and your school's policy about repeated courses. Instead stick with something like "I wasn't prepared for the rigorous studying needed for anatomy and didn't spend enough time on it. I realized I had to improve my study skills and allot more time to studying and I did much better the second time... blah, blah, blah". Most schools DO average both grades. The application process is getting more competitive every year and there are so many very strong candidates out there. Think about it... why should a school take a chance with you when there are plenty of other students who got it right the first time? So any mistake can cost you. I would suggest repeating both A&P I and II, get an A, and get as many A's in your pre-req courses as possible. Repeat the courses at a community college if that works better for you... I think most PT schools don't care where you take it, but call and check to make sure. They weigh the pre-req GPA more than the overall GPA, so spend most of your study time on those courses. It may seem like a daunting task right now, but If you really want to do this, it will be worth it in the long run.
FYI... Luckily my daughter got a "deferred" acceptance last year to the same school where she did her undergrad, so she'll be starting DPT school in January '13. We think the only reason she was accepted was because while she was there for undergrad she got to know some of the people in the graduate admissions, so they had more empathy for her situation than the other schools where she applied. She applied to more schools this year with the hopes that she would be accepted to a program that started sooner and was closer to home. None of the schools knew about the deferred acceptance, so that wasn't a factor. However, even after improving her stats and applying to several more schools, she didn't get any acceptances (so far). Good luck!