Hi Maximus....on the yorkshire terrier club of america website they give a lot of tips for grooming (
http://www.ytca.org/frame_index2.html) and clipping (
http://www.ytca.org/grooming_clips1.html) even if your puppy has cottony coat, understanding better how to treat his kind of coat will help you and him achieving a better looking coat (and less struggle) ...
Also, make sure the coat is not completely dry when you brush, like mmyorkies said, spray a little bit of conditioner on the coat (there is also a lot of detanglers made specially for this) to help get the mats out, also using the right brush helps (pin brush with a rubber backing and without balls at the ends), and finishing up my combing the coat with a metal comb.
Hope the links help you..good luck!