The first phrase is found in the Bible and refers to Jesus Christ. Perhaps a better way of understanding it is that Jesus is the uniquely born Son of God. In other words, no one else came into the world the way Jesus did, through the virgin birth. The second phrase (only Son) is not found in the Bible with reference to Jesus. The whole point of the term 'only begotten' is to emphasize the unique way God brought His humanity into the world.