What are "ha'Mabaros"?
Radak: Places to cross the water at the entrance to the city. There were towers in them to prevent the enemy from entering the city, if they will want. The verse teaches that ha'Mabaros were seized, lest one ask why ha'Mabaros did not stop the enemy from capturing the city.
Malbim: They are strongholds. This captured the conquest. After this, the soldiers were confounded and did not fight any more.
What are "Agamim"?
Radak: They are Gome (reeds) that grow by rivers. They burned them, lest the abundance of reeds prevent them from entering the city. Also "ha'Lachof k'Agmon Rosho" (Yeshayah 58:5) is Gome.
Radak citing the grammarian R. Yonah: They are fortresses. He compared this to Arabic, in which a fortress is called Agam.