@SarahGen-- Give your dog the amoxicillin and no, do not change the dose. Give it to your dog exactly as the veterinarian described.
Amoxicillin is an antibiotic and all antibiotics can cause side effects like upset stomach and diarrhea. This occurs to people as well. But there is no rule that says that every dog will develop diarrhea on this medication. Moreover, the diarrhea is temporary and will go away when the treatment is over.
Delaying treatment for an infection is much more dangerous than the diarrhea that amoxicillin might cause. The infection can get worse and spread making your dog even sicker. If you give a lower dose than directed, the medication will not work at all. So please follow the vet's direction. Give your dog bland foods like boiled rice and chicken or dry food during treatment to help prevent side effects.