As Jacob in the blessing was acting under the spirit of prophecy, he was guided more by what should take place in those tribes of Israel in the after ages of the Church, than by birth-right. See Numbers 1:32-35. And some have thought that the sons of Joseph, Manasseh and Ephraim, were types of the Jewish and Gentile Church. Hence the last is more numerous than the first. Galatians 4:27.
Related Commentaries of Genesis 48:13
Genesis 48:13-14
13 And Joseph took them both, Ephraim in his right hand toward Israel's left hand, and Manasseh in his left hand toward Israel's right hand, and brought them near unto him.
14 And Israel stretched out his right hand, and laid it upon Ephraim's head, who was the younger, and his left hand upon Manasseh's head, guiding his hands wittingly; for Manasseh was the firstborn.