I assume you are referring to the night when Jem lost his pants on the Radley fence (in Chapter 6). The children decide to make a raid at night on the Radley house in the hope of catching a glimpse of Boo. They never directly see Boo, but they do sight a threatening shadow which frightens them from the property. In the process, Jem loses his pants on the barbed wire fence, and returns home in his underwear. The children discover several new things about the supposedly monstrous Boo. Unlike most of the stories they have heard, he (the shadow) does not attempt to harm them. Boo does not attempt to follow or chase them through the collard patch. And when Jem goes back for his pants, he had two more surprises awaiting him: The pants had been folded on the fence; and
"They'd been sewed up... It's almost like--"
"--somebody knew you were comin' back for 'em."
At that moment they passed the tree with the secret knothole, and there lay a ball of twine. Although they didn't discuss it then, they must have known that Boo had mended the pants and that he had left them the gift in the tree. They were slowly coming to realize that Boo wasn't a bad guy after all. He was shy and he was kind, and he was showing them that he wanted to be their friend.