What is "Sha'ar ha'Dagim"?
Targum Yonasan: The gate of fish. Rashi - this was the name of a gate of Yerushalayim. Radak - we find in Ezra "v'Al Sha'ar ha'Dagim u'Migdal Chanan'el" (Nechemyah 1 12:39). Perhaps they used to sell fish there.
Rashi (11, citing Pesikta Rabasi 8): It is Ako, which is in the lap of fish. There, many fish are trapped. - PF)
Malbim: It is where commoners dwelled.
Really, Ezra and Nechemyah are one Sefer. They were divided into two via the Goyim, as were Sefer Shmuel, Melachim and Divrei ha'Yamim. Also the division of Tanach (other than Tehilim and Eichah) into Perakim was via Goyim. It became accepted in Yisrael to facilitate refuting heretics in mandatory debates. (Ohr Yisrael (Monsey) 5758 12, p.144).
What is "[vi'Ylalah Min] ha'Mishneh""?
Rashi: From the gate of fowl, which was second [to the gate of fish].
Rashi (11, citing Pesikta Rabasi 8): It is Lud, which was Mishneh (second) to Yerushalayim
Radak: This is Beis Midrash, like it says "v'Hi Yosheves bi'Yrushalayim ba'Mishneh" (Melachim II, 22:14); Targum Yonasan there is 'b'Veis Ulfana.'
Malbim: It is lower than ha'Geva'os (where the king and his advisors dwelled - refer to 1:10:3:3); the officers dwelled there. The wailing was greater than in Sha'ar ha'Dagim (where commoners dwelled).
What do "the hills" refer to?
Radak: These are places in Yerushalayim or nearby, like "Giv'as Garev" (Yirmeyahu 31:38).
Rashi (11, citing Pesikta Rabasi 8): It is Tzipori, which is at the top of mountains 1 like a Tzipor (bird).
Malbim: It is in the height of Har Tziyon, where the king and his advisors dwelled. The primary breakage was there.
Our text of the Midrash says 'in the hills.' (PF)