Hi, all medical schools look at both overall science gpa and overall cumulative gpa and not necessarily the gpa with what you majored in because there are pre-meds who do not major in any science. Did you get a C+ in one part of biology and a B- in the other? Maybe it's just that your weakness is in biology and that can be okay because there are people I've known who've been accepted with a C and B in Physics which is also a required course. Of course you know that anything below a C in a pre-req. is not acceptable for applying. However, medical schools will not "assume" you're simply in a tough, rigorous biology course because of those grades and let it all slide...
The difference between Physics and Biology is that Biology is more of the basis for medical school and the grade is telling in how you will do in more advanced science and medical courses. Hoping for a 13 in the biological section of the MCAT won't be that easy if you find the biology course difficult but who knows what effected those grades of yours...so, aim for the high MCAT on bio but don't count on it. The only way to show medical schools that those grades do not reflect how you perform in that science is to grab all A's in the upper level classes such as microbiology, genetics, anatomy/physiology etc. Personally I'd re-take biology if I had a C in it, there's a reason why it's given to freshmen at the beginning of pre-med because it's really a foundation type of a course...
Well, good luck with it all.