Can Logic be learned and refined in different areas?

Do you believe it is an innate human trait that develops over time? Do you think there is a difference between common sense and amount of intellect one has? The reason I ask is because I know some people that are "smart" logically (atheists by the way) and embrace science, but are some of the most irrational people I know. I'm no guru in science, but suppose someone who has intelligence that far surpes any we humans are capable of employing...do you believe that he/she will be able to have a great deal of common sense along with great intelligence? I know that common sense is logic that is "common" among the average population...but how "common" would the logic of the super-intelligent person be? Another question is, if you are able to predict one's behavior before they could reason it out themselves, would that prove that your logic is better than theirs? How about knowing what they are hiding from you in their intentions but seeing right through them?