When you fill out the application, you list all of your courses and grades. After AMCAS had checked your transcripts and verified everything, they calculate your gpa by year in college for both overall and science gpa, give you a total undergrad gpa and science gpa, a post-bac gpa (science & non-science), and graduate gpa.
Oddly, mine was a nice surprise - AMCAS calculated a higher overall undergrad gpa. Then again, I had 6 transcripts, so I probably just messed up when I tried calculating it myself. Also, I think that some schools use 3.65 for an A-, while AMCAS uses 3.7. There may be other similar discrepancies to account for upward changes in gpa post-verification.