1)
Where is "b'Ever ha'Emek"?
1.
Radak citing Targum Yonasan: 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 and close to Eretz Pelishtim 1 , and they were not walled cities; they abandoned them.
1
This is difficult. Yarden is in the eastern boundary of Eretz Yisrael, and Eretz Pelishtim is in the west! (PF)
2)
Why did they flee the cities?
1.
Malbim: 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.