Thank you for your question. My name is***** I have been a small animal veterinarian for 14 years and I'd like to help with your question.
There are really two basic causes for dogs to have itchy skin.... infection and allergies and most dogs end up having both. The infection can be with things like mites, but that is less likely and usually cured with ivermectin. It is more likely that your puppy has a bacterial or yeast infection if the skin is getting dark and smelly.
Dogs usually get bacterial or yeast infections in their skin because of allergies.... the allergies weaken the immune system in the skin and the scratching traumatizes the surface of the skin. This allows yeast and bacteria in the environment that wouldn't normally cause a problem a place to grow.
6 months is really to young to have a thyroid problem, but it is a common age to have allergies. Allergies can be a long term, difficult thing to manage, but they can be managed. There are three aspects to management. The first is treating any infection. You can get medicated shampoos online. I like Malaseb best and you can get it at amazon.com. Bath him according to the directions 1-2 times a week. However, if the infection is as bad as it sounds from your description, he probably needs oral medication too. Your veterinarian should take samples from the skin surface to see if he needs antibiotics or anti yeast medications.
Second, eliminate any potential allergens. This means put him on good flea control. It also means a new diet. Food allergy is a common allergy to onset at this age. Most commonly the allergy is to the protein so, look at what you are feeding now and get a new food... the best quality you can afford... with only 1 protein source (chicken, fish, lamb) and make sure it is a protein that is not in the food you are already feeding. Feed the new food for 3 months and see if it helps, During that time.. NO treats! just the dog food.
Third, you need to control the itch. This can be done with cortisone, but long term that has side effects. There is a new anti itch drug called apoquel that works for some dogs. Your veterinarian may carry it and it is worth trying.
I hope that helps, but if you have more questions please let me know. If not, please don't forget to rate my answer.