They look at both. They might also weigh GPA's differently according to your undergrad, Junior college vs, 4 year, etc. Some med schools put more weight on GPA, some on MCAT, etc.
Both.
Also, I'd say apx. 80% of people have a lower sci. GPA. I actually had a higher sci (3.9) than my overall (3.8). Interviewers didn't seem to care too much one way or the other. Some liked the strong sci. GPA, some seemed to think that overall was more important since it included things outside of science (which is sometimes considered important for that "well-rounded" effect. I think its just important that both are good, but especially indicative of an upward trend if GPA was lower in your early undergrad years (as is often the case)