It's not about which one is more common or less common. It is about focus.
When the subject has the focus the subject marker should be 이/가
When the subject doesn't have the focus the subject marker should be 은/는
지금 어디야 => Where are you now? The focus is "the place where you are". not "you"
So the answer should be 나는 지금 "the place" 에 있어.
The easiest way to find out which one has the focus is trying to make short answer as possible.
The word which has the focus cannot be omitted.
Or the question has interrogative and the "interrogative" has the focus.
Q)Where are you now? 지금 어디 있어?
A)School. (The subject has no focus) 나는 학교에 있어요.
Q)Who did this? 누가 이거 했어?
A) I. ( The subject has the focus) 내가 했어.
This is not all about <은/는 , 이/가> You'll come across other usages later.