(1) “Where are you from ?” and its substitute – (2) “Where do you come from?” are both correct. Your second question I think is not correctly. (1) “Where have you been?” it’s correct (without “from”) which means (2) “Where were you?” but with the difference that for (1) it’s used - present perfect and for (2) - past simple.

"Where are you from?" can either mean "Where do you live?" or alternatively "Where were you born?" I think there is maybe a mistake in the second question and it should really be "Where have you come from?" which you can translate as "Where have you travelled from?"

"Where are you from?" - This type of question is usually asked between 2 people who don't know each other yet. This denotes where you live. For example, I asked you this question, your answer would be, "I am from China." "Where have you been from?" - In this question itself is already wrong. I consider it as redundancy or overstating because you added 'from' at the end. The correct would be, "Where have you been?" "Where have you been?" - This question denotes that the 2 persons already knew each other and have seen each other already. Example, Mark and Joseph decided to have a meeting at 1 o'clock in the afternoon. In the meeting, Mark didn't arrived. At 3 o'clock, Mark arrived in the meeting so Joseph asked, "Where have you been?". Mark's answer would be, "I have been stuck in a traffic so I got here late." Anyway, Mark's answer can vary but how Joseph's asks Mark where he have been is correct. Thanks