Kuja casts Thundaga and Demi frequently throughout the fight. The damage inflicted by these spells should be easily cured by a casting of Cura or Curaga. Kuja will only use the special Flare Star magic if party members are under the Reflect status, or whether he is attacked by an ability that lowers his MP.
Flare Star is a devastating spell capable of dealing a high amount of damage to the whole party that neither Shell nor Reflect can protect against, thus it is not advised to trigger him to use it. Physical attacks equipped with the Man-Eater ability should be enough to defeat him. Successfully depleting his HP will cause him to enter Trance and cast Ultima, putting an end to the battle.