Ba'al ha'Turim and Ha'amek Davar, from Tamid 32a: What made Efrayim greater than Menasheh - in that Yehoshua descended from him ¹ - was the fact that Efrayim made himself small. ²

Rashi (citing Targum Onkelos) and Rashbam: The Torah is pointing out that he switched his hands deliberately, precisely because he knew that Menasheh was the Bechor (and that Yosef had placed him on his right).

Rosh: He switched his hands rather than the boys, leaving Menasheh on the right because he was the Bechor. Ha'amek Davar - Even though Yaakov put Efrayim first, and due to this Efrayim was the head of his Degel in the Midbar (Bamidbar 2:18); in the census in Pinchas Menasheh is first (Bamidbar 26:28-29). Also, while in the other Degalim, it says [after the head of the Degel] "veha'Chonim Alav" (e.g. Bamidbar 2:5), about Menasheh it says "v'Alav Mateh Menasheh" (Bamidbar 2:20). ¹ This shows that Efrayim precedes Menasheh only in spiritual, supernatural matters, whereas in worldly matters, Menasheh was first and greater. In the first census at Har Sinai, in which the Shechinah was above them, and the conduct was supernatural, Efrayim was first. In the census [in Pinchas] in Arvos Mo'av, when they were about to enter the Land, which was almost at the level of nature, Menasheh was first. For natural matters, the Bechor is very apt. The hand serves the head and the intellect; the leg serves natural motion of the body. 'An heir is the leg of his father' (Eruvin 70b); i.e. the nature of his father that goes by itself without thought or intellect. Therefore, Menasheh should stand to Yaakov's right.

Hadar Zekenim (to 48:18): Some translate as, 'even though Menasheh was the Bechor;' just like the word 'Ki' in the Pasuk, "La'Shem... ha'Selichos Ki (even though) Maradnu Bo ² " (Daniel 9:9).

Ohr ha'Chayim: [He wanted to put his right hand on Efrayim. He could not see well enough to recognize him, but] he inferred that Menasheh is on his right, for he is the Bechor (and Yosef assumes that he will get the bigger Berachah).

Malbim: The Zohar says that in Birkas Kohanim, the right hand must be above the left. Yaakov should have put his left hand on Menasheh, and afterwards his right hand on Efrayim, and it would be on top. Rather, he put his right hand on Efrayim, and afterwards his left hand on Menasheh, so it was on top. His hands showed that he knew that Menasheh is the Bechor; even though the right hand is on Efrayim, the left hand was above, on Menasheh, to show that he does not draw his influence of Berachah via Efrayim, rather, through his own conduit.