I don't have a puppy but I do have a dog I was worried about. So while they were chicks I had them in my bathroom, I would let her in to smell them, hear them and sit in the bathroom while I cleaned their area etc. I also made her sit still while they hopped around her. Then when I took them outside for the first time, I did it in a plastic tub and let her hang out with us but not get too close. As they got older I let her interact more but always with me by her side. She has done amazing and now thinks of it as her job to keep them safe. She stands with me, herds them (gently) with me and keeps a close eye on them to make sure they aren't causing trouble. She never barked at them. She whined a bit when they would squawk but that was more of her worried whine.
But I do have a funny story about barking at funny chicken noises.. I now have four roosters. I got six babies around the same age and four of them are definitely roosters. The two older one's are crowing. They make this hilarious crowing sound that is just hard to explain. Anyways, every morning now while I am putting on my make-up all I hear is.. *strange crowing* *bark bark bark* *strange crowing* *bark bark bark* My dog can't figure out for the life of her what that hideous noise is and barks every time the rooster crows. So funny, so annoying!