When using the Ballista do not hold down the fire button. It is more effective to rapidly tap the fire button as it makes the bolts shoot out faster and the archangel boss fight at the end of chapter 3 easier.
Extra Armour Components
You can add extra components to your armour by scrolling to the last section of the 'Update' screen.
Potions
Before attempting the Ballista section make sure you have plenty of potions or you will die a lot.