Both are correct. 화장실은 어디예요 is natural if you have talked to someone before and continue the question. (By the way,) where is the bathroom? 화장실이 어디예요 is natural if you just ask question to someone who you never talked to before. (Excuse me,) where is the bathroom? For more information, refer to https://www.italki.com/question/462379

you can use both of them.

you can use both of them.