Well, you definitely would know better than me. I'm not any kind of a programmer. I'm only guessing because of reading the difficulties that others have using the API to right mission scripts and assume that what we're talking about here would be a lot harder.
When PA panels absorb damage 20%, rounded off, does actual damage to the panels. The rest is absorbed and stored as power in the panel. If a volley of more than 3pts per pa box strikes the panels in a single volley and the panels are at reinforced levels (They have 2 power levels that they can be run at, standard and reinforced.) then a "leak pt." of damage is scored. 1st on hull, if available, then using the DA chart if there's no more hull hits.
If a pa box is destroyed the power that it was holding is transferred to other boxes in the same panel bank if they can hold it. If not, then it goes to an energy module if the ship has one. If no energy module is present then it goes to another set of pa panels on a different bank of the same ship. If there aren't any other panels available to hold the power, either because they are already full or they aren't powered, then the excess power would go to either the batteries of the ship or to the pa panels of a satship, if powered, in it's hanger, at the players option. If none of these options are available then the released power would be applied as damage. You can also shut off a panel bank and follow the same procedure to deal with the released power.
At the end of a turn 10% of the power stored in the panels can be transferred into the ships batteries and 1pt of power per pa box can be dissipated into space if the player so chooses.
Considering that we don't even have proper shield repair in SFC, I just assume that PAs would be really, really hard to get right. I'd love to be totally wrong about this though. I only mention it as a point of discussion, not to be argumentative.