Hi and welcome to Just Answer. I am a licensed veterinarian and will do my best to help you.
Is the hair sort of sticking up in circular patches?
Is it in multiple areas and about the size of a quarter for each one?
How much does your dog weigh?
These sound like hives, an allergic reaction to something, frequently a food item. Here is further reading on hives: http://www.petplace.com/dogs/allergic-reaction-from-an-unknown-cause-in-dogs/page1.aspx I would give benadryl.
Benadryl is dosed at about 1 mg per pound 3 times daily. See this article on this product:http://www.petplace.com/drug-library/diphenhydramine-benadryl/page1.aspx