I suggest to stay away from using Auto when fighting bosses...
As for fighting the dragons... Each one has a different type of breath that causes certain problems. Just so long as you have a white/red mage to heal and you have them negate the negative effect, you'll do fine. By the time you fight the dragons, you should have an item to equip your red/white mage with that item. A white mage could work better as you can use Esunaga if your other characters are in a bind.
Also, make sure to store up on Bravery... Too low on brave points can be problematic.
Mega Zygarde = Midgard Serpent eating its Tail Hello, I am Aura of the Opal.
My setup is Pirate with Hunter(Dragon slayer), Whitemage/Spiritmaster with Greater fairy ward(To counter those eye magicks) and another with spiritism for Stillness(Use in a bind) and the last for a swordsman(Anything really, just another attacker) all equipped with anti whatever status effect they inflict. Be warned that this setup is slow and isn't effective against the dark dragon.
edit: Ineffective cause I don't have enough courage rings. Can't seem to find a shop from which to buy.
"Corn-cob-man? There's a lot of sick people in this town."- Red Guy