Arcana Coelestia # 6282
6282. 'May he bless the boys' means, May he make it possible for them to have truth and goodness. This is clear from the meaning of 'blessing' as endowing with truth and goodness, for in the spiritual sense 'a blessing' does not imply anything else, 1420, 1422, 4981; and from the representation of Ephraim and Manasseh, to whom 'the boys' refers here, as the Church's understanding and the Church's will, to which truth and good were to be imparted, truth to its understanding and good to its will.
Three
The number three in the Bible represents completeness. That's why Jesus rose on the third day after the Crucifixion -- his transformation was complete. It's why Elijah stretched himself on the dead child three times, why Jonah was in the belly of the fish for three days, why the Lord called Samuel three times, and many more. It's also reflected in the fact that there are three levels of heaven, three levels of hell, three levels to human life and, ultimately, three aspects of the Lord Himself: Father, Son and Holy Spirit.