when I first got Dooney- she got batted quite a few times especially by our large 20 pound male cat. Keep treats on you at all times, when the puppy goes after the cat tell her to leave it until she comes back to you and then give her a treat. Now when i first started doing this, Dooney would run after the cat, automatically stop and come back to me waiting for a treat, so i started randomly treating her.
She likes to play "grab Jake's tail" when she comes in from outside and he waits by the door, when she is outside-its almost as if he likes it. Today Jake rubbed up against her, it has been 3 months. Just be consistent with what you do.