Hi newbie! 😀
How low are we talking about for prereqs? If it's C- or lower, definitely consider retaking. Some med schools require grades of C or better in the prereqs.
For the AMCAS (MD) application, retakes are averaged.
AMCAS example:
Biology I (Fall 2003): F, 4 credits
Biology I (Fall 2004): A, 4 credits
AMCAS calculation: C, 8 credits
For the AACOMAS (DO) application, only the most recent grade (regardless if it's higher or lower) is used.
AACOMAS example:
Biology I (Fall 2003): F, 4 credits
Biology I (Fall 2004): A, 4 credits
AACOMAS calculation: A, 4 credits
and
Biology I (Fall 2003): C, 4 credits
Biology II (Fall 2004): D, 4 credits
AACOMAS calculation: D, 4 credits
Regarding the certificate program you're considering, the way that it will affect your GPA will depend on whether it is composed of undergrad courses or graduate courses and how many courses count as science (biology, chemistry, physics, math for the MD application; biology, chemistry, physics for the DO application). If the courses are undergraduate-level, then the courses will be calculated in your undergrad numbers. If the courses are graduate-level, then the courses will be calculated in a separate section, Graduate, on the MD application. Therefore, this Graduate distinction can be bad (because it doesn't affect your undergrad numbers at all) or good (because it gives you a new slate, so you have another "new" GPA). I'm less familiar with how graduate grades play a role in the DO application. The path you should choose will depend on your existing academic record, your financial situation, and the time you're willing to spend to reach your goals.
There are a lot of enrichment/enhancement programs out there. Some help your undergrad numbers, some help prep for the MCAT, others are rigorous graduate programs that simulate the 1st year of med school, some are mixed undergrad-grad. These programs include one-year certificates, one-year master's degree programs, one-year certificates, one-year certificates with the option of staying an additional year for a master's degree, two-year masters programs, and the do-it-yourself method. The program that's best will vary from one individual to the next.
The more info you're willing to share, the more input you'll receive. 🙂