lol, ALL new rats will do that! They're scared, they don't know where they are and they have this giant pink thing with five limbs trying to pick them up all the time, and they never know where you're taking them. How would YOU feel if a giant hand picked YOU up all of a sudden and you didn't know where it was taking you? However, if you know you can TRUST the hand, then there's really no issue, is there?
The best way to gain a rat's trust is to let it know that GOOD THINGS come from you. Let it know that YOU give it food and YOU give it water. Gradually "bribe" them out of the cage with treats and eventually it'll sit right in the palm of your hand. Oh, and use carrots--most rats LOVE carrots.
Like codcommando said, it'll grow out of it. I just got a baby rat myself (Choco), and he's still pooping all over the place too...but my older one (Yuki) taught Choco from day one that I'm someone to be trusted. Once again, a really cute story that I'll save for another time.