Will 2 Cs hurt my chances at good schools? (not Ivies, and things like that)

I am a Junior this year, and I got a C in AP Calculus AB this year and the same in AP Physics C Mechanics. One teacher taught both. He was really bad, and family issues made it worse. I have a 3.9 GPA and a 98/325 rank. I am trying to get a 34-36 ACT, and have really strong ECs (Eagle, NHS, Community Service, Leadership, Clubs, and shadowings), LORs, and essays. And because of those two Cs, I am taking two dual credit classes at my local college. My GPA won't decrease with the DC, but will increase very little. I also think that I got a 4 on the AP Physics C Mechanics exam. I plan on taking easy courses in semester one of my Senior year to boost my GPA before college apps.

But will those Cs look bad on the transcript and hurt my chances?