Someone posted a very exhaustive explanation of the damage allocation interactions of various weapons with the special types of shields and armor a while ago. Maybe one of our local BB wizards can *bump* it up again.
Basically, when there is any 'left over' damage that isn't enough to actually destroy a component it's stored somewhere and ADDED to the damage done by the next weapon to hit that ship. Special effects like shield regeneration or armor regeneration are then applied AFTER the fact. So it is possible for the damage on a ship to be effectively 'healed' because the previously accumulated damage is added to the current weapon damage, and THEN this is canceled by the regenerated shields. This can also result in a huge amount of damage being "carried" from armor into the inner vitals of your ship if you've got enough damage to almost destroy a large armor component and are then hit with an 'ignores armor' weapon, for example. The damage is ADDED to the ignores armor weapon and then the damage is applied inside your ship. 100+ points in a single hit. Ouch. It is a messy system, and I think MM has gotten a lot of complaints about it. It's probably a major logical puzzle to make all those special abilities work appropriately in all situations.