How will B’s in honor classes affect college admissions. I have had 2 B’s in two semesters of Honors courses while getting straight A’s in the 6 APs that I’ve took so far. What would colleges think?
Just as how your GPA shows.
Where are you aiming for?
I am aiming for some of the elite universities such as Stanford and UChicago. 1580 SAT and decent ECs. How bad will the B’s look?
That you got 2 B’s. In the 10 minutes or so that they take to read a college app, they will not spend much more time analyzing that. Having said that, if the balance of your application is sufficiently strong, and they deem you an applicant that they would like to have, a B or 2 won’t really matter.
They will think you got two B’s. They will also see that your SAT reading scores are below their average at 690 (from another thread) along with your 800 math. Nobody can predict admissions outcomes at very competitive schools, many of which have acceptance rates under 10%. Do your best to make your application stand out in a positive manner.
Other than that like everyone else you should apply to a wide range of reach, match, and safety schools that appear affordable (run net price calculators) and that you would be happy to attend. There are tons of amazing colleges out there that can give you a great 4 year experience and get you where you want to go in life.
The grades probably have by far a greater impact if they relate to your stated major/emphasis (assuming you give one). For example, a B in math or science courses can hurt you a bit if aiming for elite engineering programs, while if you are a prospective humanities or arts major then not so much. Either way, however, you get some brownie points for taking the harder courses offered at your school. If you were an engineering student, it might very well be better to get a couple of B’s in the most advanced math and science courses then to deliberately (and obviously) avoid those courses, take an easier non-honors/AP curriculum, and get A’s.
It’ll depend on all other factors. Don’t worry about two B’s. You’re not expected to be perfect. 
Stop thinking about this, don’t worry.
Much more important is finding your two affordable safeties and affordable matches, discussing budget with your parents…