Forthe school that get 10000 Apps...BU, GT, GW, Drexel...I think they are the ones that will reject you if your GPA falls under a certain level...3.0 maybe
I would guess that they probably would screen by overall for that, but past the initial screening and at other school, my guess would be they take both into account when deciding who to interview, accept, reject, etc.
I think science GPA is more important when it comes to evaluating non science majors. If you are a science major, chances are your science GPA is gonna be similar to your overall gpa, just because you are gonna be taking a buttload of science classes. (not true in everyones case, but I bet in the majority)
However if you are a humanities major and only take the prereqs...You could have a 3.8 GPA, but only have a 3.0 Science GPA. That will definitely raise some questions