Changing the various parts of your ship is similar to changing equipment in an RPG game. Each part has a direct effect on your ship’s stats, which you can see in things like damage output, maneuverability, and speed.
Every faction in Aqua has a different approach to war, so it’s up to you to decide what strategy you’ll employ. Do you prefer small and fragile, but fast and deadly scouts? Or rather slow and heavy, but damage resistant siege ships? If you’re looking for something in-between, your best choice is a fighter- which compensates its average stats with secondary weapon slots.