Having a couple of C's shouldn't significantly impact your application as long as you do well during the rest of your undergraduate career and finish with a strong BCPM GPA (Biology, Chemistry, Physics, and Math). Schools will see your year-to-year trends for your overall GPA and BCPM GPA so doing well during your junior and senior years will help.
See if you can switch to Physics for Life Science Majors. Either way, make sure to maximize your resources for Physics II. Go to office hours for your professor and TA, see if there's tutoring options on campus, form study groups, etc.