In chapter 26 Scout and Atticus have a minor discussion about Boo Radley. Most of the paragraphs in the beginning are her thoughts on how she's changed her thoughts about Boo. It's not so terrifying to her anymore. She even "felt a twinge of remorse, when passing by the old place, at ever having taken part in what must have been sheer torment to Arthur Radley--What reasonable recluse wants children peeping through his shutters..."
She goes on to fantasize about how it would be if she were ever to see him. She wonders about their conversation and how they'd act. The only conversation she has with Atticus is a brief mentioning to him that she'd like to get a quick glimpse of him before she died.
What he reveals is that he knew all along that Jem had lost his pants that night--and that the 3 of them were running around Boo's backyard. He says to her, "You know Mr. Nathan shoots at every shadow he sees, even shadows that leave size-four bare footprints. You were lucky not to be killed."
That is how he shows her that he knows a lot more about the incident than they ever suspected he knew.