Why does Yakov bless Ephraim and Menashe at the same time? Why not bless them one after the other?
Before answering this question from the sefer בני יששכר we need to mention two more problems that the commentaries raise:
The posuk in Bereishis (48,14) says that although Yosef placed Menashe on Yaakov's right and Ephraim on Yaakov's left, Yaakov deliberately crossed his hands and placed his right hand on Ephraim and his left hand on Menashe. Why did he not have them switch places instead of crossing his hands?
And the posuk says that the reason why he crossed his hands was "because Menashe was the firstborn". But if Menashe was the firstborn, then on the contrary he should have placed his right hand on Menashe!
But the Bnei Yisasschar explains that each month of the Jewish year has one of the tribes associated with it, and the three months of Tishrei, Cheshvon and Kislev are associated with the tribes of Ephraim(Tishrei), Menashe(Cheshvon) and Binyamin(Kislev), the three tribes who came from Rachel.
Now, there are altogether three Batei HaMikdash (Temples). The first was inaugurated in Tishrei the month associated with Ephraim, the second was inaugurated in Kislev the month associated with Binyamin, and third and final temple will be inaugurated in Cheshvon the month associated with Menashe. This third temple is the main temple of the three, and this is alluded to by the sign of the Zodiac which is associated with this month, the sign of the scorpion (Scorpio) which in Hebrew is called עקרב which is עקר ב, that is, the עיקר בית (the main house).
The first temple was actually completed in Cheshvon, the month in which the inauguration of the main temple is supposed to take place, but its inauguration was pushed off until Tishrei, the month of Ephraim. This is why Yaakov placed his right hand on Ephraim, to show that first temple which is associated with Ephraim would precede the main temple that is associated with Menashe, the firstborn.
Thus, the only way all this could be alluded to in Yaakov's blessing was by blessing them together, so that by placing Menashe on his right he showed that he was more important because he was the firstborn and so the main temple was to inaugurated in his month, and at the same time by crossing his hands and placing his right hand on Ephraim he showed that the temple that was associated with Ephraim was to precede that of Menashe.
And thus when the posuk says that he crossed his hands because Menashe was the firstborn, it means that he crossed his hands rather than have them switch places because Menashe was the firstborn and so had to be placed on Yaakov's right.