They're just two ways of asking the same question. I think that the former may be ever so slightly more formal, but the distinction's pretty mild. However, the second sentence ends in a question mark. That's colloquial. In Japanese, questions are formally written with periods.

''どこにいますか？'' doesn't specify the you, so depending on the context it could mean someone else. There is probably more to it, but that's all I can say/explain with certainty.

One is 'Where are you?' and the other is 'Where are (you) going?'.