In order to better understand how damage is dealt, I did some extensive testing with the simulator. Here are my results, in FAQ format:
1. How is damage assigned?
First, ignore shields for now (see Question #2). Now, every time you hit a ship, a random component is selected on the target. If the target still has armor, the random component will be a piece of armor. Now, if the amount of damage you've done with that hit equals or exceeds the damage resistance of the component, it is destroyed. If you have left-over damage, another component is randomly selected. Repeat until a component is selected for which not enough damage remains to destroy. This extra damage is stored by the target for use later.
Now, next time the target is hit, the first thing that happens is any extra damage (from previous hits) is added to your weapon's damage. Then, the selecting of components to be destroyed occurs as described in the above paragraph.
As you can see, this means components do not have "damage done to them." I have not been able to verify it, but it is likey that when a component is randomly selected and not destroyed, it is remembered and automatically selected in the future until destroyed. This would give the appearance of a single component taking damage. However, I do know that if you change damage types (say from normal to armor skipping) a new component is randomly selected.
That means, if you modify Armor III to take 400 (instead of 40) damage to destroy and change the Shard Cannon to do only 1 damage (it skips armor) and then hit a ship with one Armor III for 300 normal damage (which cannot destroy the piece of Armor III and so sits around as extra damage) and then hit the target for only 1 point of damage with the Shard Cannon, 301 damage will be randomly targeted at components inside the target's armor!!! This is why Shard Cannons and Null-Space Projectors sometimes really gut ships, especially those using high-resistant armor (Organic, Crystaline, etc).
Of course, the reverse is also true. If you hit with armor skipping damage but fail to destroy a component, you just generate extra damage. Future hits may apply that extra damage toward armor, even though it originally skipped armor.
2. Ok, so how do shields fit into this?
I'm glad you asked. First, don't mix phased and non-phased generating components. If you do, you get non-phased shields. That is, until all the non-phased shield generating components are destroyed; then suddenly, in the middle of battle, your shields will become phased.
Ok, otherwise, shields work just like you expect. Damage from weapons gets taken off your shields first. However, remember above where I told you extra damage is added to your weapon's damage before being applied? That happens before your weapon's damage is applied to shields. That means, hit a ship with normal shields and some Armor III with a PPB (skips non-phased shields) for 35 damage (not enough to destroy a piece of armor) and then with a Meson BLaster (normal damage) for 30 and the extra damage (35 from the PPB) is added to the Meson's 30 for a total of 65 damage delt to the target's non-phased shields!!!
This gets even more fun with shield regeneration. See, if you get some damage passed their shields without destroying components (so it's still extra damage), but the regenerators bring the shields back up, that damage you got passed their shields gets pulled back out and has to go through the shields again next time the ship gets hit.
As an added bonus, destroying a shield generating component drops your current shield value to your maximum shield value (assuming your current value was greater than max value) but it does this
before the component is destroyed! This means, with 3 Shield V (900 shields), if you get hit by a PPB that kills one of the generators, your shields will be 900 out of 600! If a second hit kills another generator, your shields will be 600 out of 300.
3. Um, I'm afraid to ask, but how the @#$!% does Organic Armor work?
Ready for this? You're not, but I'll tell you anyway. Each ship with organic armor regenerates constantly. Every turn. Even if you take no damage. With no cap. Put 10 Orgnaic Armor III (30pt regen/turn each) and
every turn it gets credit for 300 points of regeneration!!! By the end of turn 5, it has 1500 points stored up with which to repair organic armor. That means, on turn 6, if you deal 1500 damage, you'd destroy all 10 of his Organic Armor III's. Then, before turn 7 begins, all 10 would be completely repaired!!! The repair would cost all 1500 points stored up so far, though.
This is why organic armor seems so incredible at first, then suddenly seems to give out without warning. You are coasting on the built up regeneration for the rounds of combat while you were closing range.
The good news is, destroyed organic armor does not contribute toward this regeneration total. So, in the example above, where all the organic armor was destroyed, no regeneration would be built up at the end of turn 6, because all the organic armor is destroyed. That means, on turn 7, if the ships takes another 1500 damage, destroying all its organic armor again, that's it. It used up all its regeneration pool to repair the first time, and hasn't been able to build up any more, so you're out of luck for the rest of the fight.
Also note that only destroyed organic armor is repaired. Regeneration is never spent on partially damaged armor, because, as you recall from Question #1, components cannot be partially damaged, only destroyed.
4. Do I really want to know how Crystalline Armor works?
No, you really, really don't. But here it is. Let's do this by example. Assume a ship with 0/300 shields and 4 Crystalline Armor III (150 damage resistance each , 15 dmg converted to shields each) and no damage inside shields yet. This ship is hit by a Meson BLaster (normal damage) for 30. The CA regenerates the target's shields by 30 (it could have done up to 60, but the weapon damage was only 30). This shield regeneration is done
after the weapon damage is applied against shields, so it doesn't block this hit. Now, the 30 weapon damage becomes extra damage since it cannot kill the armor (that takes 150). So, we now have 30/300 shields and 30 extra damage.
The target is hit again for another 30 damage. First, we added extra damage to this, so we get a hit doing 60 damage (see Question #1 if you've forgot about that
). Now, the shield blocks 30, so 30 damage is left which causes the CA to regen another 30 shields and the ships extra damage to be set to 30, again. So, we now have 30/300 shields and 30 extra damage. Look familar?
That's right, if you cannot, in a single hit, do either 150 damage OR more damage than the CA can convert to shields, you will NEVER hurt the ship without armor skipping weapons (see Question #1 for how much fun you can have sneaking non-armor skipping damage inside a ship with armor-skipping weapons).
Don't believe me? Ok, example continued, but doing 60 damage this time. Adding extra damage makes it 90, shield blocks 30, 60 points of shields regen'd and 60 points to extra damage. Now we have 60/300 shields and 60 extra damage. Hit again for 60, plus extra damage is 120, shields block 60, 60 left, regen shield 60 and extra damage becomes 60, leaving us with 60/300 shields and 60 extra damage? Fun, isn't it?
Again, 65 damage though. Add extra damage, 125, shield blocks 60, 65 left, regen shield 60 (max for 4 CA-III) and extra damage set to 65. Hit again for 65. Add extra damage, 130, shield blocks 60, 70 left, regen shield 60 and extra damage set to 70. Hit again for 65. Add extra damage, 135, shield blocks 60, 75 left, regen shield 60 and extra damage set to 75. As you can see, the extra damage slowly creeps up, and once it hits 150, it will kill a piece of CA. At which point only 45 damage can be converted to shields and doing 65 a hit, the ship will begin to die faster.
Now, here is the scary part. We're 60/300 shields with 75 extra damage and no CA destroyed yet. You've been slowly chipping away with 65 damage weapons. Guess what happens if you hit is for 60 or less damage? Hit for 40. Add extra damage, 115, shield blocks 60, 55 left, regen shield 55 and extra damage set to 55. Now we're at 55/300 and 55 extra damage. That's right, the ship has effectively healed 20!!!
Moral of the story, once you've got his shield almost down, fire *only* weapons that do more damage than he can convert to shields (or do 150+ damage). If you must use lower damaging weapons, fire only your highest low-damage weapon until his shields equal the damage that that weapon does. Then, switch to your big guns. This maximizes the amount of damage applied to his components. If your "big gun" happens to be armor skipping, even better. This will suck the extra damage from your weaker weapons right past his armor into his internals. Also, armor skipping also does not trigger CA's shield regeneration. This makes it the ability of choice for taking out crystalline armored ships.