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
Start the fight by shooting Ares and then dashing right through him. Jump and glide over him while shooting down towards him. After gliding over him dash which will make you end up on the other side of the screen. Keep shooting while watching Ares carefully. If he does his lightning attack back off and wait for it to end , then fire at him again. If he starts firing at you go back to jumping and gliding over followed by the dash like before.
Once you get Ares to 50% health he will jump in the air and fire a large electric shield around him. Back far in to a corner and wait for him to drop to the ground. Be ready to dash through his bullets now ( this is the critical part of the fight )
Dash through then run back 3 times. On the 3rd time stand still a few paces away from the very back of the stage. Ares will charge you , jump up above you , when he does this its your opportunity to fire off 1 or 2 shots , then immediately dash to the other side. DO NOT dash to the end of the screen , leave some space so Ares can jump over you. Ares will now shoot the 3 times like before. I suggest double jumping over the first shots. then standing still for the second shots and finally double jumping over the 3rd shots. Now once again stand still and as Ares jumps over you shoot him. Rinse and repeat this method until the quicktime event and end of the boss fight.