There is a place on the Common App to note AP exams taken and ones you plan to take in May of 12th grade. There is also a space to note the score.
Your son should write about his uneven performance and his great strides this year in the additional information section of the Common App. If he won't, ask his GC to write about it in their recommendation.
I have two in college, but I'm not familiar with colleges with supportive environments. However, there certainly are a number of schools with supportive environments, and I would search such topics on College Confidential. There are plenty of kids like your son on College Confidential (or probably their parents) and they have found colleges that really "get" kids like him. You want a school where he won't be just a number, someplace that is looking out for him and knows when to step in and help him.
It sounds like he has grown a lot in the past year - kids can surprise you. My middle kid is a college freshman, and she never used to speak up when she needed help to sort out a scheduling snafu, never used to follow up on emails and calls (especially when the other person - the paid professional adult - should have been doing that), etc. She has had to do these things the first few months of college - and while she still complains when others mess up or forget stuff - she just takes care of things.
Good luck in the college search.
