I'm hoping chemguy79 or kcwang will see this thread. 😀
Based on what I know about PharmCAS, your overall GPA will be calculated based on every class you've taken, undergrad or masters. It breaks it down based on subject & year, as well, so the school can see that information.
You will still have to report your undergrad information - I don't think it's an "instead" situation. However, schools may consider your masters GPA more important or may consider an upwards trend. I think the best advice would be to contact your prospective schools, let them know you'd like to do what you need to be a competitive applicant, and see what they say.
You may have an uphill battle - unless you have some sort of "in" independent of your undergrad performance, getting into a masters program might be tough in the first place. Best of luck in your endeavors, though! 👍