Both questions are somewhat ambiguous. You're trying to write: "how ARE you doing at school?" In the same meaning: "How are you doing?" in a general sense, right? So, you shouldn't write: "como você esta indo PARA a escola?" this preposition indicates the movement or how to getting around toward the school. But if that's the meaning is correct. But if you're interested in how the person is having school performance, learning, liking or disliking, as it's felt about that, so you say: "como você esta indo NA escola?". I hope this helps. :)

"Como vai a escola?" or "Como vão os estudos?" is how we'd say "How are you doing at school?" in Portugal.