That depends on whether you are applying to allopathic or osteopathic programs. For allopathic schools the two grades are averaged. For osteopathic schools, if you re-take a course only the most recent grade is factored into your GPA, NOT the best grade out of multiple attempts.
So for example if you take bio 101 and get a B- the first time and a C+ the second time, allopathic schools will average the two, whereas osteopathic schools will only count the most recent attempt, which in this case is the C+, despite the fact you did better the first time.
One other thing to note is that osteopathic schools do not take math classes into your science GPA, therefore it is only BCP.