Help my rat is aggressive, and attacks my puppy

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Mr. Pedro- Sancho- Diaz......

Barked: Tue Feb 9, '10 10:36pm PST 
I have a 3 year old rat terrier. I rescued him from a lady that kept him outside with WOLF puppies....Latley he has really gotten teriorial with my room, House etc. I recently got a 6 week old puppy, and when they are on the bed together, My ratt snaps. He has bitten the puppies face and caused blood...Have any of u out there, had this problem with aggression or territory issues? and what is the best solution. SO far I am isolting them!