The first is fairly common when speaking about someone's circumstances, such as their financial state, their job title, or their history. Basically it refers to being in someone's shoes, so to speak.
He's buying a brand new car with all those debts he has? I wouldn't do
that if I were in his position.
The second isn't common at all and the only way it works is if you're talking about someone's physical location. I can't even think of a good example for it.
John's on the US/Canadian border and he's going back into the US? I
wouldn't do that if I were at his position.