Ship Item Placement

Damage is applied to Shields > Armor > Inner > Outer. Only Inner and Outer slots can suffer directional damage, so placement will have a minor effect there. The decks are merely there to provide extra slots and have no other effect.

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Space Empires Depot | SE:V Balance Mod

It seems to me that whenever I had something at the top left corner or a ship it was always destroyed first.

I don't know how the multiple decks adjust damage on each component, I know it's annoying as heck to take what looked like a grazing shot at first and see 2 clean decks only to look again and see on the deck I didn't view all engines are damaged so bad that my super-fast scout is knocked down to a speed where it is easily overrun and killed, but I can say for a fact that stratigic item placement can be the difference between a good, long lasting design and a totally worthless design. For the ship to fly, it has to have a bridge and Crew. If these go out, the ship's pretty worthless, so I design my ships so that just about everything gets destroyed before either of these. The rest of my ship is designed based on it's role. My scouts have their life support and supplies as the next layer, my close range defensive warships have their guns and ordinance there. The closer to the inside of your ship things are, the less likely they will loose that component without completing their combat role.

Damage is directional irrespective of decks

So if you're ship strategy is to lead the chase, put all your engines at the front and sacrificial comps at the rear