Why did David put the Aron on a wagon? Bnei Kehas did not get wagons, for "they carry the most Kodesh matters (including the Aron); they will carry on the shoulder" (Bamidbar 7:9)!
Rashi (from Sotah 35a): Because David called Divrei Torah "Zemiros" (Tehilim 119:54), he was punished, and erred about something that even children [who learned only Chumash] know. Therefore, when he brought it [afterwards] from Beis Oved, they brought it on the shoulder. He told the Leviyim "Hiskadshu
Why does it say "El Agalah Chadashah"?
Radak: This is like Al, and similarly "va'Yach Es ha'Pelishti El Mitzcho" (Shmuel I, 17:49, is like Al Mitzcho), and "El he'Harim Lo Achal" (Yechezkel 18:6) is like Al he'Harim.
Why was it a new wagon?
Radak: [It is proper to use for the Aron] something that a commoner never used. It was made for Kedushas ha'Aron.
Were they conducting the wagon?
Radak: They were conducting the cattle that were pulling the wagon.