whatever is on your record they look at. there's a reason why they have all those separate categories. but i think the more important one is science gpa. i think the first 2 they look at is overall and science GPA.
Though I'm fairly sure overall science GPA is more important, I know that some schools, LLU for example, separate the GPAs into each subject - I was able to see my application printouts. Surprisingly my Bio GPA was much higher than my sGPA, and my Chem GPA was much lower - came to a bit of a shock when I saw it broken down like that, hehe.