Okay, so, while second years don't necessarily have to be in the same class, if you wanna be in 2C then go right ahead. First years and third years will be in rooms starting with 1 and 3 respectively, so feel free to decide which class your characters will be in. Also, any NPCs (such as Headmistress Serizawa or Tsukuba-sensei) can be freely controlled by anyone. And if you need to create an NPC for, say, club advisor or anything, go right ahead.