Where is "ba'Emek"?
Radak (Shmuel I, 31:7, citing Targum Yonasan there of "Ever ha'Emek"): In the side of the plain. I.e. they were in the plain close to Eretz Pelishtim. Also Ever ha'Yarden are the places close to the Yarden 1 , and they were not fortified cities; they abandoned them.
Malbim: It is Yizre'el, where they fought (Shmuel I, 29:1).
Radak's words imply that they are close also to Eretz Pelishtim, but it is difficult to say so. Yarden is in the eastern boundary of Eretz Yisrael, and Eretz Pelishtim is in the west! (PF)
Who did they see had fled?
Malbim: [The soldiers of] Yisrael.
Why did they flee the cities?
Malbim (Shmuel I, 31:7): They saw that they cannot rely on the strength of the nation, for they fled, and not on the king, for he and his sons died.
