You will need to know the amp/hr of the 6v Trojans vs the 12v. Simple math leads you to take the configuration that produces the highest amp/hr output. However, 6v cells are larger than 12v cells and most will tell you that the 6v batteries give more stable power and have longer life.
Hopefully there are some big boat guys online that can share their experiences.
2006 Bayliner BR205
A1 Gen 2 1.47
5.0 carb engine