How does "la'Eifod ve'la'Choshen" fit with "Avnei Shoham" and "Avnei Milu'im"?
Rashi: "Avnei Shoham" refers to the Eifod (which comprised two onyx-stones), 1 and "Avnei Milu'im" - which means 'filling-stones', to the Choshen. 2
Ramban: Both "Avnei Shoham" and "Avnei Milu'im" refer to both the Eifod and the Choshen. 3
Targum Yonasan: The onyx-stones are synonymous with the Avnei Milu'im, and they were used both for the Choshen and for the Eifod.
Da'as Zekenim: There was also an onyx stone in the last row of the Choshen.
Hadar Zekenim and Da'as Zekenim: This is similar to the Pasuk in Tehilim 113:6 "ha'Magbihi La'sheves ha'Mashpili Lir'os ba'Shamayim u'va'Aretz", where "ha'Magbihi" applies only to "ba'Shamayim", and "ha'Mashpili", only to "u'va'Aretz".
Why were the stones of the Choshen called "Avnei Milu'im"?
Rashi and Rashbam: Because they filled the settings that were made for them in the Choshen. 1
Ramban: The onyx-stones were called "Avnei Milu'im" inasmuch as they had to be complete stones, 2 as opposed to the stones of the Eifod, which were allowed to be cut. 3
See Ramban's many objections to this explanation.
In fact, Chazal learn from here that the engraving of the twelve tribes and the names of the Avos on the Choshen had to be performed by means of the Shamir worm, which cut into the stones without detracting anything from the stone itself (Ramban).