Treating a Shih Tzu's Yeast/Bacterial Infection?

I have a two year old Shih Tzu, who has bad yeast and/or bacterial infection. I lived in a wood floor home before moving to a carpeted home a year ago and that is where and when all the problems started. First fleas, now he is on pills for that. But now the skin condition is back and I need something as strong as amoxicillin, but healthy. Does anyone have great ideas that have worked for you?