In my experience, most people only ever say "how you doing" as a joke, if they're trying to sound funny or creepy. It depends on the area, though. In some places and cultures in the US, it's be common to hear people ask, "Hey, how ya doin'?" Unless you're from one of these areas or part of one of these cultures, it will sound weird for you to use this construction. (It would sound weird if I said it, because I don't have the right accent to say it in a natural way. It would sound like I was acting.)
"How are you?" and "How are you doing?" are both fine. In informal situations, a lot of people will also say "How's it going?"