Dear Lu,
It's not likely that mild SI issues will have any causal relationship to encopresis in any direct manner, but in a more general sense children with SI limitations can lag a bit in various areas of development.
Be encouraged that your son has used the toilet successfully. From a behavior management point of view, the best approach is to be patient and to
supportSupport
Support 500 and reinforce the type of behavior you want. This can be easily done with a five-year-old by establishing a simple incentive/reward system, using a chart with stickers, and then offering your son a small reward on any instance that he uses the toilet.