It's all up to you. Then, with the weapons schematics you've designed, you can automatically construct a real projectile at any time during battle with your ship's molecular assembler. So the action-packed combat is similar to any other action game. Mass and Energy are the respective amounts of your ship's matter and energy stores required to construct one projectile during battle. Payload refers to the flavor of pain that a particular projectile inflicts upon the unlucky recipient.
Propulsion is the means by which a projectile propels itself from one place to another.
Projectiles with propulsion types that have high thrust values cannot turn very quickly, and so they will perform poorly at homing onto a target. But such projectiles do have the benefit of being very speedy. Note that mines cannot have any propulsion. Trigger is the means by which a projectile decides when to detonate. All projectiles explode when they receive damage, such as upon impact, but a trigger allows a projectile to go boom for other reasons, too.