One of the advantages of putting the children in the front row of the balcony in Harper Lee's novel To Kill a Mockingbird, of course, is that this postion provides them with a perfect overview of pretty much the entire courtroom. It also subtly suggests that these Finch children and their friend Dill are more closely allied with the blacks in attendance, as they too believe that Tom Robinson is innocent.
Because the novel is told from Scout's perspective, the author sometimes has to invent ways for Scout to know what is going on. More than once, for example, the young character overhears adult conversations that she would normally not have access to. In this trial scene, she is similarly able to overhear the exchanges and survey pretty much all of the action while being out of Atticus' field of vision (see the speculation in Chapter 17 about whether or not their father could even see them, should he turn around and look). She seems even to enjoy the vantage point, even if she doesn't understand the significance of every event in the trial: "from [our seats] we could see everything," the narrator states in Chapter 16.
Jem and Scout sit in the segregated section of the courtroom: in the balcony with the black population of Maycomb. When they first arrive at the courthouse, they cannot find seats. They're disappointed, because they think they'll have to stand. But Reverend Sykes finds them.
"There's not a seat downstairs. Do you all reckon it'll be all right if you all came to the balcony with me?"
"Gosh yes," said Jem. Happily, we sped ahead of Reverend Sykes to the courtroom floor. There, we went up a covered staircase and waited at the door. Reverend Sykes came puffing behind us, and steered us gently through the black people in the balcony. Four Negroes rose and gave us their front-row seats.
So they're in the balcony, but they're clearly treated with respect by being given the front row seats. They don't really mind being in the balcony...I don't think they see anything unusual about it. In fact, Scout describes them as "happily" following Reverend Sykes. So they're excited to be there. Jem may know that it wasn't custom for white children to be up there, but Scout doesn't really think about it. They don't think anything about it until Aunt Alexandra scolds them later.
Scout and Jem sit in the segregated section of the balcony with the African Americans. When they first arrive they think they might not have seats, but the Rev finds them and tells them to sit with them. They do not think about anything until they are scolded by their Aunt but they are simply happy to be there.