More than likely he is upset. Once someone is frustrated with and tired of talking to that person because they cannot convince them to do something, they they will same something like "do whatever you do" or a version thereof. "do whatever you want to do", or "you do whatever". The other slight possiblity is the opposite meaning, but very rare. Someone for example may be a genius at something let's say playing a game with his friend on the computer and his friend is equally smart. And let's say the the genius asks his smart friend for some advice on what to do next, to go to the next level. His friend, who is smart too, may look at his friend and say "do whatever you do", because he has faith in his friend, and the friend doesn't know either on what to do, so he will say "do whatever you do". This is a positive statement then. There is a third option. You may ask someone what they feel about you doing something. The person you are asking couldn't care less and will then say "do what you do" and they really mean it in a neutral manner. They really don't care what you do, go ahead and do it. They may care about you, but really many people don't care what you do and will say that and mean it in a nice way.

If he didn't say "blah blah blah, do whatever you do" then more than likely it was more neutral in nature. And perhap even positive, because the person WANTS you to make up your own mind, the person WANTS you to "do whatever you do".

It sounds demeaning... saying "...whatever you do" could imply that this person thinks that what you do is not very interesting or important. It implies that he is not interested in the details, he just wants you to do it and not bother him. If we had a little more context, it is possible that it was not meant this harshly.