The fire of Miss Maudie's house takes place in chapter 8. Up to this point, the children were obsessed with one thing--to get Boo Radley out of his house. Slowly but surely the children began to get closer. That did this in spite of what Atticus said--leave Arthur Radley alone.
By the time of the fire, the children had done a lot. For example, Jem lost his pants escaping from the Radley yard when Mr. Radley shot a gun at them, thinking the children were trespassers. The children also had contact with him though knothole in the tree.
So, when Boo Radley came out during the fire and placed a blanket around Scout, Atticus knew that the children had interacted with Boo. Also during this time, Jem's guilty conscience could not bear his disobedience any longer. He confessed to Atticus all he had done. Here is the text:
"Jem seemed to have lost his mind. He began pouring out our secrets right and left in total disregard for my safety if not for his own, omitting nothing, knothole, pants and all."