We find in the last part of Bereshit that, just before Yaacov Avinu passed away, he blessed Yosef sons and made them his sons.
How do we understand that a grandson becomes a son? Can we apply it in our days and if not what was the real reason for this?
Looking at the source in the Torah (Bereshit 48:15-16) seems to indicate something else. It isn't that Yaacov Avinu is making the sons of Yosef his sons. It is that he is praying to the Creator that the 'Redeeming Angel' that looked out for Avraham, Yitzchok and himself, would also continue to look after these children of Yosef.
Yaacov wanted the angel to include Yosef's children in that protection that had come to the rest of the family as a result of their relationship to Avraham, Yitzchok and Yaacov. Since Yaacov didn't make a similar prayer for the other grandchildren who already existed, it must be assumed that Yaacov didn't have a question about them receiving that angelic protection. And this seems to follow the Targum Yonatan on Genesis 48:16:
יְהֵי רַעֲוָא קֳדָמָךְ דְמַלְאָכָא דְזַמִינְתָּא לִי לְמִפְרַק יָתִי מִכָּל בִּישָׁא יְבָרֵךְ יַת טַלְיָיא וְיִתְקְרִי בְהוֹן שְׁמִי וְשׁוּם אַבְהָתַי אַבְרָהָם וְיִצְחָק וְהֵיכְמָא דְכַוְורֵי יַמָא סַגִי מִסְתְּגֵי בְמַיָא כְּדֵין בְּנוֹי דְיוֹסֵף יִתְקְפוּן לִסְגֵי בְּגוֹ אַרְעָא
An angel behaves strictly according to the orders that it was given and doesn't diverge from that mission at all.
Taken in context, this would suggest that something about the specific status of Yosef's two sons was different from the rest of the family in Yaacov's view.
To understand this properly would require close examination of the relationship of this particular angel to the Avot and the details of how it was commanded to interact with Avraham, Yitzchok and Yaacov.
Rav Hirsch points out that when Reuven lost the bechorah, the three elements of that status were split among three other children. The kedusha aspect was given to Levi. The tribe of Levi even in Mitzraim were treated as the "priests" of Bnai Yisrael and did not have to serve as slaves. Yehuda was given the status of Malchus and from him would come the final dynasty of kings and the Mashiach. Yosef was given the "double inheritance". Thus, Efraim and Menashe were treated "like Reuven and Shimon" to be counted as two of the twelve tribes. Note that when Levi is treated as part of the tribes, Yosef is treated as one. When matters of inheritance, such as dividing the land, or the census in the desert are dealt with, Efraim and Menashe are treated as separate tribes and Levi is not included.
Yosef was the bechor of Rachel and should have been the first born of Yaakov. That is also why he received "shechem echad" (often translated as an extra portion) over his brothers.
See What is "birthright" really? for more on this subject.
Targum Yonatan says (about Reuven):
But because you sinned my son, the birthright is given to Yoseph, the kingship to Yehudah, and the priesthood to Levi
There are two complementary comments in Rashi that explain the mechanics. One in chapter 35 vs 11 and more at length in chapter 48 vs 4.
Basically, Yaakov had a prophecy in parshas Vayishlach in which he was told he would produce another גוי and גוים. The גוי was understood to mean Binyamin once he was born. Once it was clear that he would not be having any more sons, the גוים was understood to mean one of the tribes would be split into two.
This promise was viewed as a gift from Hashem. A gift which Yaakov subsequently re-gifted to Yosef on his deathbed.
Rashi's words are based off the Bereishis Rabba 82 4.
