안녕하세요. :) We use both of "어디에 있어요?" and "어디예요?" for asking other person's location. It seems no much difference between two of them. But They are slightly different. "어디에 있어요?" is asking for a specific location rather than "어디예요?". A : 어디예요? Where are you? B : 강남이에요. I'm in Gang-nam, is the big one area in Seoul. A : 어디에 있어요? Where are you in/at? 
 B : 커피숍에 있어요. I'm in a coffee shop. This preposition "-에(in/at) ; can be omitted" can make a more specific question because it asks not only where you are also where you are IN. It has also a slightly different tone and situation. 지금 어디에 있어요? Where are you in/at now? There may be some situations I have to know where you are in this moment. It can sound urgent for the same reason. 지금 어디예요? Simply asking where you are.

They are both specific about the location, with largely the same meaning but somewhat different feel. 어디예요? is a common way to ask where someone is. It can be taken as "거기(가) 어디예요?" or "지금 있는 곳이 어디예요?". It has a casual feel, almost like a greeting, and you would answer (여기) XX예요, where XX is the name of the place. 어디(에) 있어요? sounds a little more serious, so you can use it when it is important to know it or when you have been wondering about it.