Our children may not understand everything we can about God - but they can understand something, and you should take this seriously. Jesus said, "Let the little children come to me, and do not hinder them, for the kingdom of God belongs to such as these" (Mark 10:14).
What can a child understand about God? For one thing, our children can understand that God is real, and that He made the whole world - including them. They also can understand that God loves them. They know what love is, because they experience it every day from their parents - and in the same way, they can understand that God loves them, and they can pray to Him.
In addition, they can understand that Jesus was a real person who walked on this earth many years ago, and that He came from heaven to show us that God loves us. And they can understand also that God knows what is best for us, which is why we should follow His rules for living.
Let me encourage you to bring your son to church, and also to any classes your church has for children his age. But most of all, put Christ at the center of your family - and your life. Then let your son see that Christ makes a difference to you - as you pray before meals, as you read stories from a children's Bible to him, and as you let Christ influence your actions every day.