Malbim: Here it says that he passed one son, for he acted to anger Hashem, and one who passes all his children is exempt ¹ . Divrei ha'Yamim teaches that later he passed his other children. To avoid being exempt, he passed his second son by himself. The exemption of Kol Zar'o is when he gives all of them in a way that is liable, i.e. via the priests ² . There it says "b'Gei Ben Hinom", to teach that in every case he was in Gehinom (liable for his actions). His son Amon (whom he did not pass, for he succeeded him as king) was born after Menasheh repented. He was 22 when Menasheh died (33 years after he repented).

Radak citing Pirkei d'R. Eliezer 43: He removed the Heavenly fire, which descended in the days of Shlomo, from the Mizbe'ach.

Malbim: All of these abominations of the Kena'anim were to anger Him. There is no Hana'ah from them, and they were not b'Shogeg!