Johnny is one of those itchy dogs too. He first got this way when he was about 6 months old.
After feeding a rabbit/potato or venison/sweet potato and using Temaril-P and Atopica, still having an itchy dog, and not happy with the side effects, we went to a holistic vet. I had forgotton that Atopica suppresses the immunity system and that it takes about a month to work in the dog's system.
Since the dog is still itchy after eliminating the foods that could cause the problem, the allergy must be from a different source.
The vet prescribed hydroxyzine, an antihistimine without He gets it mixed with peanut butter.
YUMMY!!! After 5 days, I can say the itching/scratching is down 25% but he's still in transition and still taking Atopica every other day.
The vet also suggested giving the heartworm med and flea-tick application several days apart. I've read some of the flea-tick products make the dogs feel like their skin is crawling with bugs.
It's so frustrating and it seems there are so many dogs suffering this way.
Good luck with whatever you decide to try.