Is there any difference between あなたはどこですか。and どこにいますか？
あなたはどこですか。 Where are you?
どこにいますか？ Where are you?

Is there any difference?

Question

Is there any difference between あなたはどこですか。and どこにいますか？
あなたはどこですか。 Where are you?
どこにいますか？ Where are you?

Is there any difference?

Answer

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.

Answer

''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.

Answer

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

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