Hey-
Call them and ask!! Well, I think that most kids come in with some AP credit whether it be in the sciences or in the non-sciences. I think that AP works well to get some college classes out of the way while you are still in high school. I used it for a history class for example and it opened up a little more wiggle room in my liberal arts curriculum. In terms of AP for the pre-med sciences, I used an AP calc, which most schools don't need. But then I took calc II and this showed that I pretty much must have done college level in the AP class in order to jump in to calc II and do well. I had AP credit for physics but then I retook the first semester only so that it would refresh me for the second semester, for I had only received one semester. I liked physics so I figured why not take it and get a good grade in it.
So, I think that colleges will not look down on AP especially if you have done well in the upper level portions. Such as organic for exempting chem... AP is for good students and I think med schools realize that hey, these kids worked hard in HS and paid to get credit at the college level by taking the AP test. If you check the website of the school you are applying to they usually have whether or not ap can be used. Just be ready to know the stuff on the mcat. Remember to call the school and ask. Don't worry about it.
