1)
Why did he call him "Elokei Yisrael Yoshev ha'Keruvim"?
1.
Malbim (Yeshayah 37:16): You rule over all upper and lower legions; it is known that You are G-d via Yisrael, who serve You; Your Hashgachah is most apparent between the Keruvim. It is proper that You fight Yisrael's battle for Kedushah of Your name!
2)
Why did he say that only Hashem is G-d over the kingdoms?
1.
Malbim (Yeshayah 37:16): This is unlike Sancheriv said - "where are the gods of Chamas