Eugene's second form isn't that much harder, but it's definitely longer. Have Mag use Strike Hammer and boost his stats with Gre's skills. I personally prefer Pepper over Chain, and Gre definitely is a must for this fight. Have Gre heal the party with Cheer Up and use items if you need (Naolin+ and Mokona Ampoule are useful for this fight).

Prince Eugene has about 7000HP.
Moves: Fire Rollin' Bomb [May cause sleepiness],
Ancient Light [Cancel all your effects],
Knock Down,
Nail,
Naolin 1500 [Enemy restores 1500 HP],
Autrishclaff.