First things First , do not attempt the perfect boss runs until you have maxxed the Photon Launcher. Also if you get hit by the boss , simply die and continue and try again. The checkpoints are just before each boss in the game
Method for the Boss Fight
As the fight starts keep shooting the boss at an angle. After he goes under the first time he can do several different attacks. Keep shooting up and to the left while standing near the edge.If the boss comes up behind you duck and turn around and keep shooting. At the halfway point the boss will go underground again. Push LB when asked to , then just keep looking for the rubble where the boss will appear from. Keep jumping and dashing away from where he exits while shooting him.