Hi there Charles!
Your first sentence can be used, but I personally would use "How have you been?" so it leaves room to the person to say if he/she is okay or not. But then, it´s just a detail, a personal taste here.
Now, to the "why the the HAVE?"
1) it is used in this way (present perfect) when you mean something that happened in the past, at some point in your or somebody else lives, before now. And you don´t think it´s important the exact time the action happened.
2) it is used to talk about actions that began in the past and have duration up until now.
So, the kind of question you wanted to know, initially, certainly fit on 1) and 2)http://www.englishpage.com/verbpage/presentperfect.html
Are you ok?
You are using the presente simple with verb TO BE usually when we ask questions that can be asnwered with YES/NO. Of course, if you want to know something at the spur of the moment, or
the general state/condition of someone (how he is doing/how life is treating him/her).http://english.stackexchange.com/questi ... n-question