I am treating one of my feet for athlete's foot. Do I need to do anything to my shoes in order to limit/prevent it from getting worse, or coming back again after it clears up?
It is possible your shoes are harboring the fungus, but the reality is, the fungus is pretty much everywhere in the environment--gym and shower floors, elsewhere on your skin, etc so eliminating the fungus is only a temporary thing. Some people use a antifungal powder or spray inside the shoe daily.
More important is to use socks that are breathable (non-synthetic) and white socks are better than dyed socks. When the weather is better, staying "sockless" in sandals is best of all.