When Scout leads Boo Radley to a shadowed chair, she is showing respect for the fact that he doesn't like to be in the light. This could mean a variety of things. First, he doesn't want attention directed to him. Second, he is literally bothered by light after living in the basement and not coming outside for years. Third, a shadow is a sort of shade or ghost to a child. This is what Boo had always been to the kids: a phantom. Now, to Scout he's real.
A few moments later Scout narrates:
I led him to the front porch, where his uneasy steps halted. He was still holding my hand and gave no sign of letting me go.
"Will you take me home?"
He almost whispered it, in the voice of a child afraid of the dark.
I put my foot on the top step and stopped. I would lead him through our house, but I would never lead him home.
Scout at this point does go with Boo to his house, but he escorts her there. She realizes she cannot relate completely to his circumstances and that people are all different. We must respect those differences and she gave him the control from this point. This world he stepped into with the rest of society for a few moments is one that he may have very well been afraid of, and she respected that giving him the courtesy of a friend to walk home with and nothing more.
There is much irony in these moments as Scout moves from fear of that which is different to respect for the difference.
she shows him respect of being hidden