dog allergies???

Question
Our new 3 month old puppy appears to have a skin allergy.  He has been with us 1 1/2 weeks.  We are visiting a local veterinarian who is treating 2 patches of skin that were raw on his neck when we got him. They are much better, however, we've noticed he is constantly scratching/chewing himself.  The vet checked for mites. Negative.  He doesn't seem to have anything so we believe it might be allergies.  Is there something that is almost always the culprit with dogs?  

We feed him "I AMS" puppy chow and do NOT feed him people food. He doesn't seem to be losing hair in those itchy spots as yet, but his white fur gets orangey/brown in those spots from bleeding just a bit.  Mostly he chews around his paws, lower areas, rear.  Could it be from our carpet being scotchguarded?

 We hate to put him on medication if it is something we can do something about. I am just wondering what to do for him.  Thank you for your expertise.

Answer
It is extremely rare for puppies to have environmental allergies.  Usually, if they do have allergies, it is to a food or a particular protein.  If that is a possibility, then ask your vet to change him to Purina's HA diet, which is the only commercially available hypoallergenic diet for young puppies.

More likely, however, is that the scratching is from sarcoptic mange.  Even though your vet said that the skin scrapings were negative, over 75% of these pups with mange will scrape negative.  Ask him to treat the pup for sarcoptic mange anyway.