You should say "How do you do?" when you have met someone for the first time. This person replies with the same phrase. And you say "How are you?" when meeting someone you already know. The reply is often "Fine (thanks). And how are you?".

"How do you do?" is a bit more formal than "How are you?" Kirk is correct, "How are You?" is something you would likely say to someone that you already knew, though it would not be improper to say it to someone you were meeting for the first time. I think it would be similar to dzien dobry / czesc.