I'll try to make a list of all Clone Commanders from ROTS : where they are fighting and under what Jedi General they are serving before Order 66.

I'll try to be very precide but If find some error or discordance feel free to post a comment.

Commander Odd Ball: Battle of Coruscant under Genaral Obi-Wan Kenobi

Commander Cody: Utapau under General Obi-Wan Kenobi

Commader Gree: Kashyyk under Genaral Yoda

Commander Bly: Felucia under Genaral Aayla secura

Commander Neyo: Seleucami under Genaral Stass Allie

Commander Baccara: Mygeeto under Genaral Ki-Adi-Mundi

Commander Appo: Coruscant under Lord Vader

Commander Thire: Coruscant under Emperor Palpatine