Hi there- not sure what your exact situation is, but I am doing something similar. I matriculated and am working towards a 2nd bachelors (although I am only taking the science courses I need to apply to med school and that are specific to my second degree), and my grades will count towards my undergraduate GPA. Any classes you are retaking now will be averaged with whatever your original mark was when you apply. As long as you are not working towards a graduate degree, my understanding (anyone else correct me if I am wrong) is that your additional grades will be factored into your undergrad GPA when you apply. Just as a helpful hint (having no idea about your circumstances/reasoning for non-matriculation), if you apply as a matriculating student, you are eligible for financial aid. 🙂 Also, registering as a matriculating student does not necessarily mean you need to complete the degree- it doesn't matter either way as long as you take the classes you need. But if you want the degree, your undergrad credits transfer and should exempt you from the school's core curriculum so you can just take the classes you need both for med school prereqs and the degree requirements (this is the way my school does it, at least- I'm not sure if all universities operate the same way).
I found it very helpful to talk to the prehealth advisors at my school before applying- they are very familiar with non-traditional students taking classes after graduating and will be able to walk you through any specific details as to their requirements/program.
Hope this helps, and best of luck!
