Schools have different policies about "not doing well" in the prereq courses. Obviously, if you failed either chem or bio, you would need to retake those, because you wouldn't have technically completed those courses.
Some schools require you to have at least a C in all prereqs. Others don't care, as long as you have at least a D-, have done upper level work, have a convincing reason for having done poorly, and have convinced them that you are past the period where you were performing badly. EVERY MED SCHOOL IS DIFFERENT. I know that schools have very different procedures from applying this past year and speaking to admissions directors at schools I didn't get accepted to (in case I had to reapply, I wanted to know specifically what they would want to see me do -- but I did get in to med school so I'm all set!

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<B>I would call the med schools</B> you want to apply to and ask their policies regarding grades less than C's. While it may be embarrassing, you would be able to find out which schools you shouldn't bother to apply to if they won't look at you because they don't consider that you have satisfactorily completed the official pre-med requirements. The other possibility is that if you REALLY still want to apply to a school that has that policy, you could take those courses again during the year you are applying, and tell them that you are in the middle of taking the classes and you will update them with the grades.
There is this pre-med resource that I think is the coolest: A woman who was the director for admissions at New York Medical College answers pre-med questions (from their specific situations) on this website:
http://www.examkrackers.com/forums
I think she (Judy Levine) has mentioned something about adcoms not being *psyched* about community college courses, but I don't really recall. You could read the answers she gave to other students, and even ask her yourself for her opinion on what she thinks you should do.
But I would say, after applying (blech), my biggest piece of advice would be to call schools to see if they'll even consider you given your grades in those classes. It could save you a lot of money, and time, and ego, and let you focus more on the schools that will take a more comprehensive and balanced look at who you are, what challenges you've overcome and how you are achieving now, and how great a physician you'll be.
Good luck.