The choice of antibiotic is based on the system (respiratory) you want to target, the suspected organism involved and the discretion of the veterinarian based on previous experience. While Clavamox is widely used in veterinary medicine I have not found it to be predictable in treating respiratory disease of puppies. If your puppy is already on Clavamox it is best to stay with that for 5-7 days and gage the response, if he is not improving then changing to another antibiotic may make sense. Keep in mind we are looking for improvement in symptoms in a few days not necessarily resolution of all symptoms, that could take a couple weeks.
Each veterinarian has a different set of experiences that help to guide treatment decisions. In my experience doxycycline, cephalosporins or erythromycin derivatives have often worked well.