How old is you pup and how long has it been since he has been brushed. I think the secret is treats treats and more treats....
They make lots of conditioner for dogs. You can go to the pet store and get some until you find what you like. Never brush the babys hair when it is dry. Always moisten the hair. I put conditioner in a spray bottle and spray her before I brush. Also you can spray the knots to help. If its too bad you may have to have it shaved so you can start new.