If the Ivy accepted your son, he did not “over-reach” (I hate that comment). They saw success in his application.
Our kids went to an Ivy and a top LAC from our basically just-adequate high school–they were under-prepared. Both breezed through HS. They do both write well, though (I teach college writing, so that helped. 
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D initially went to a less competitive OOS flagship and then transferred to the LAC. She did a lot of extra researching and work to keep up with the other kids. Her major required a lot of history knowledge, for instance, and we didn’t have AP Euro or World, and it seemed like everyone else knew stuff she didn’t. So she’d go to the library after classes and look up everything that came up in class convo, along with another friend from a similar school. (like ducks, paddling like mad underwater though looking like they’re gliding). She ended up PBK, but worked her backside off to get there.
S had an up and down experience for personal reasons (depresssion), but when he worked hard, he got A’s at his Ivy. When he had issues, he didn’t. Working hard was necessary for him to excel–again, he had to start from a different place from most of the kids from the “better” high schools. He finished strong after some time off and was a prof favorite because he enjoyed classroom discussion and writing about complex ideas.
So I agree with others that it’s not the HS at this point–your S1 will figure out that what he needs to do to close the gap is different from the “better prepared” kids, but that he has the smarts to do it–he wouldn’t be there otherwise. So I think that’s what you should emphasize to him–getting the work done and going for help when needed.
People have given you great ideas for S2 to supplement. I would just add to discuss this same thing ahead of time–learn to recognize when you’re behind the eightball and figure out what you need to do to catch up. If he knows that this is likely as he begins at his eventual college, he’ll be ready to tackle it and succeed.