Why does it say "va'Yishlach ha'Am Shilo"?
Malbim: They did not ask Shmuel, and not the Urim v'Tumim, whether they may remove the Aron from Kodesh ha'Kodoshim.
Why does it say "Aron Bris Hashem Tzevakos Yoshev ha'Keruvim"?
Radak: "Hashem Tzevakos" means that He is Master over soldiers, to strength His lovers and weaken His enemies. "Yoshev ha'Keruvim" means that He is "close to all who call to him in truth" (Tehilim 145:18). If not for Aveiros, it would have saved them. Refer to 4:4:4:1. "Yoshev ha'Keruvim" teaches that it had Keruvim on it, and the first Luchos in it, according to all opinions (refer to 4:4:2:1).
Malbim: This hints that the Aron should be under the Keruvim 1 , and not on the battlefield.
This implies that they took the Aron without the Kapores (its cover, to which the Keruvim were attached. - PF)
Which Aron was this?
Rashi (Devarim 10:1): Normally, the Aron that Moshe made [for the second Luchos] accompanied them in war. This time, the main (Betzalel's) Aron was taken. Radak - it held the second Luchos. The broken Luchos were in Moshe's Aron; it says about it "v'Aron Bris Hashem Nose'a Lifneihem" (Bamidbar 10:33). 1
Ramban (Devarim 10:1): It is the Aron that Betzalel made. It housed the second Luchos and the broken Luchos. 2 Moshe's Aron was hidden once the Luchos were transferred to Betzalel's Aron.
This is like R. Yehudah ben Lakish in the Beraisa Meleches ha'Mishkan (Perek 6) and Yerushalmi (Shekalim 6:1). Tosefta Sotah 7:18 and Rabanan in the Yerushalmi hold that the whole and broken Luchos were in the same Aron. Da'as Zekenim, Hadar Zekenim, Rosh (in Devarim 10:1, 10:1, 10:2) - before the Beis ha'Mikdash, all agree that they were in separate Aronos.
Radak: This is like Bava Basra 14a.
Why does it say that Bnei Eli were with the Aron?
Radak: This teaches why the Aron did not save them, due to the sins of Chofni and Pinchas. They caused this debacle. Malbim - and from there (on top of the Aron) came Hashem's word that they will die the same day.