I certainly need to remove the internal armour as it was part of the old armour rules. I am just not sure yet how to replace it. One option is the same as the new magazines, where you can increase their HTK by adding armour. This means I don't have to track actual damage to internal armour but it makes internal systems harder to destroy at the expense of space. I could do that with engines, power plants and turrets. Another option, as you mention above, is to have separate "sections" of armour covering different parts of the ship but that would increase the complexity of both design and damage resolution quite a lot. It would also mean more armour was required for the same level of protection.As an example, five 10m3 spheres have more surface area than one 50m3 sphere so more armour would be required to cover them all to the same depth. I think the HTK system is probably the better option but I am open to ideas.
Internal armor won't ever be thick enough to worry about tracking damage to it. I think that it can be simulate quite easily by just increasing the HTK of a system.
If someone wants to have an armored section of their ship then just armor several systems and declare that they are in the same section in the fluff text.
One thing that would add realism but will add programming complexity is the ability to armor some portion of a set of system components. Thus, have a few engines or a few life support modules in the armored section and the rest outside the armored section.
BTW, I glanced up and saw that my browser was flagging "armour" as a misspelling. My first thought was that my typos were making me look like a Brit. Then I realized that the "typos" were in Steve's quoted text. I may be slow but I get there eventually.
Still, I had to resist the urge to spellcheck them into "proper English." <grin>