How much of my transcript do top schools look at?

Your GPA is really strong which will definitely help you. If you are interested in how much different colleges care about test scores, GPA's, demonstrated interest, etc, google "[Insert college name] Common Data Sheet" For example, Harvard Common Data Sheet. If you go to section C7, it will tell you how much this university relies on certain things for admission! Best of luck!

If by "top schools" you mean Ivies or similar schools (something like the Top 30 on US News), then we usually consider their unweighted GPA range to be a 3.7-4.0. Not sure if your 3.9 would be weighted or unweighted, but if it's unweighted, you'd be well into that range and should be fine from an academic standpoint, assuming that your test scores were also at the high end. (The rough benchmark is a 1500+ SAT for most Top 30 schools, 1550+ for Harvard/Yale/Princeton/Stanford/MIT.) In the end, multiple Bs are fine—plenty of people get into these schools with a few lower grades as long as their GPA is still over the threshold and the rest of their application is strong.