וישלח ישראל את ימינו וישת על ראש אפרים והוא הצעיר ואת שמאלו על ראש מנשה שכל את ידיו כי מנשה הבכור.
Rashi has difficulty with the word “ki” and explains it as “im ki” (although). But the Targum says “arei – because”.
I heard a good, alternative explanation (don’t recall the source).
The verse means Yaakov didn’t want his actions to be obvious”because” Menashe was the firstborn. Why should the Bechor be made to feel inferior by being pushed leftward? But once Yosef spoke up, the sleight of hands was revealed even to those bowing their heads, so Yaakov had no choice but to give a little speech (again showing kind consideration to Menashe, saying גם הוא יהיה לעם וגם הוא יגדל).
If you read the pesukim, I think you will find this all fits very well.