Will colleges care about this?

I want to major in chemistry in college, but in my sophomore year, I got two Bs in my Chem Honors class. I got 2 As in AP Chem, will get a glowing rec from the teacher, got a 5 on the AP Test, and will retake the subject test which I got a 770 on (June 2014). In addition, I also was top 2 in my school for Chem Olympiad, tutored other students in chem, and won several awards in Science Olympiad for chem related events.
Will my 2 Bs hurt me or leave me with nothing but a slightly (ok actually by .05) lower GPA?

No. Whether you get accepted or rejected will most like not be due to 2 B’s.

No those B’s won’t hurt you. You have been doing better and better in Chemistry and you have shown a sustained interest in chemistry.