Yaakov's preference of Ephraim over Menashe seems to be yet another blow against the special status accorded to first born children, following the long series of such blows recorded throughout Tanach. Yitzchak "wins" over Yishmael, Yosef over his brothers, Moshe over Aharon and David over his older brothers.
The Kli Yakar says that the above examples imply Hashem's preference for the weak and oppressed. On a larger scale, this is why He chooses Bnai Yisrael over the mightier and stronger nations of the world. Rav Samson Raphael Hirsch explains that the better, not the older or stronger, will triumph. The winners will win because of a greater spiritual accomplishment, not because of the "accidental" concept of a birthright.
In the world of idol-worshipers, the firstborn became the patriarch, or the special priest, and gained much of the inheritance. Chazal tell us that Yaakov's actions are a lesson to the Jewish people that we should base rewards on merit and righteousness, and not merely on who is born first. For Jews, spiritual superiority is far more important than other factors.
When Yosef told Yaakov that he was putting his hand on the wrong son, he didn't realize that Yaakov was not taking Menashe's birthright away from him, as Yosef's brothers had tried to do to him, but only representing who was superior in Hashem's eyes. When Yaakov responded, "I know, I know," he meant that he understood Yosef's fear, and assured him that the removal of Menashe's birthright was not his intention.
May this be a lesson for us to always strive to be the best in the eyes of Hashem, and not merely in the eyes of our fellow men.