Since page numbers can vary, I'll include the chapter for the quotes below.
Scout is most comfortable in pants and a casual shirt. She enjoys being outside and finds that dresses don't allow her the freedom to participate in her favorite activities. This is a great concern for her aunt, who believes that Scout should dress like a proper young lady, but Atticus doesn't take issue with it. Neither does Miss Maudie, who is Scout's confidante.
In chapter 24, Scout is expected to attend her aunt's missionary circle meeting, so she is forced to dress up. Upon seeing her, Miss Maudie asks, "Where are your britches today?" Scout quickly replies, "Under my dress." This elicits laughter from the group of ladies, but Scout is confused; she hadn't meant to be funny. This demonstrates how out of her comfort zone Scout feels in a dress. Although wearing "britches" under a dress is not ideal, it allows her to feel a little more like herself than she would otherwise. A few moments later, Miss Stephanie asks whether Scout wants to grow up to be a lawyer, and Scout dismisses the idea, replying that she just wants to be a "lady." Miss Stephanie scoffs at this comment, telling Scout that she "won't get very far" if she doesn't "start wearing dresses more often." Scout is taken aback, and Miss Maudie holds her hand for strength.
Women and girls wouldn't begin wearing pants in mainstream American society for several more decades. Scout's choice to defy social norms is indicative of the way Atticus has raised her: to throw off the expectations of society and to find her true sense of self.