Remember that atmosphere is a combination of setting and tone. Look at the descriptions of the house and Boo Radley himself and consider the fact that everything comes from the perspective of children (or their versions of Miss Stephanie Crawford).
The darkness of the house (physically created by shadows and lack of street lights and socially created by the neighborhood's lack of knowledge and relationship with the Radley's), the prejudice of the town, and the interest of the children, suggest a negative atmosphere surrounding Boo Radley. Some descriptive words for this atmosphere might be mysterious, intriguing, and possibly evil. The incidents with the tree, Jem's pants, and the blanket on Scout (at the fire) however, suggest a positive atmosphere surrounding Boo. This seems to be an atmosphere of innocent secrecy that comes with good intentions. It is almost a childish secrecy, the kind that every child enjoys, almost as if there is a prize for solving the mystery.