Fish, Adcoms and Pharmcas take into account all of your science class, including of your 12 units (by units I assume you mean credits. For example, I needed Phy 1 & 2 for my pre-req, but I also took intro to physics and that was included in my Science GPA and my overall as well. Anything and everything that is science related will be used to calculate the science GPA, (along with the science credits) will be used to calculate the overall GPA.
This means that your bad non-req grades will definitely lower your overall GPA and if they were science related courses (even if they're not a pre-req) they will affect your science GPA. This does not mean its the end of the road for you, but you should take this into account when you wish to re-take some classes, if that's what you want to do.
As far as replacing (by replacing I assume you mean retaking a course), Pharmcas doesn't not grant grade forgiveness. This means that the bad grade and the good (replaced) grade will be included. So if you earned a F the first time and an A in the retake you average out to a C for that one course.
Gooner, I think you will be ok. Make sure the rest of your app is somewhat strong. That means experience, essay, LOR's, etc.