"Do you go to school already?"
Translation:Вы уже ходите в школу?
should be correct. report it.
btw just noticed the connection between your avatar and username.. lolz
Ты уже ходишь seems more likely - who would use вы with a child who possibly doesn't even go to school yet?
I think it's because it's a direction (to school) not a location (in school); it answers the Куда question, not the Где one.
Accusative is used for directions and prepositional for locations.
When using verbs of motion like to walk or to drive, the words following prepositions are in accusative instead of prepositional