Does the clean kid manual work for kids with encopresis?

Talk to a specialist. Encopresis can be an especially trying and difficult disorder to treat. The specialists in treating it usually are either behavioral and developmental pediatricians or pediatric GI doctors. They will be familiar with various approaches, probably including the clean kid manual. You need to have someone you trust with whom you can work towards a longterm solution.
Depends on cause. Many conditions cause encopresis. The most common cause in normal kids is adhd. Poor habits, diet, fluid intake, fear are the other causes. Kids with spina bifida have difficulty evacuating. Rarely, hirschsprung's disease is the cause or other rare intestinal problem. Cleankids was written by a psychologist who approached the fear and bad habit angle, but not the medical causes.