How do you defeat jacomo, folon, and ayme on that ship?

Yes, you can beat Giacomo and his goons at pretty much any level.
I suggest you use good Magnus. The highest attack, the highest defense, and the best healers. Take powerful cards from your non-battle buddies and give them to your three fighters. Refrain from putting many Combo 2+ cards in, because it can be a pain in the neck to fight if you don't have a Combo 1 card to start it off. Try not to have too many offense-only cards, too. A good balance is imperative to win. If you want specifics, I'd say 1/2 or less offense, about 1/4 defense, and about 1/4 healers per person. Meaning, don't make Xelha carry all the wine and fruit, Lyude hold all the shields and Kalas use only swords. Make sure each battler has some of each, especially ensure someone has death-healing Sacred Wine or the Holy Grail.
Finally, if you fight them and die, retry. Before you get out of the deck altering screen, give yourself what you found you needed. I noticed I had way too many Combo 2 and offensive Magnus, so I got rid of some and put in Combo 1 shields and armor.

You can do it.