I believe the procedure is to roll all of the firing ship's weapons at a target.
Then when the attacking ship is done, if the target ship is damaged (loses 1/3 of hull) or crippled lost 2/3 of hull), you make the rolls to see if weapons, thrust, ECM, etc are degraded.  Now later in the firing sequence of the turn, any addidional ships that fire at this previously targeted/damaged or crippled ship will fire at it as it now is changed; if ECM is gone, it now is easier for the second, third, fourth ship (whew!) to hit.  If shields were weakened by the bombardment of an attacking ship, any ship after that gets easier penetration rolls.

This is an advantage of two 500 point ships vers one 1000 point ship.  No matter what, all of the shots of the 1000 point ship will hit/penetrate/cause havoc on the target as it was when firing started. 
For two 500 pt ships:  The first fires, and if it damages/cripples (the term we use here in Jacksonville is "causes a threshhold check"; it comes from FullThrust) to the target ship, then when the the second ship fires, after the other side has fired a ship, then it may fire at a weakened/degraded ship hitting &/or damaging it easier. 8-)

Hope this helps.
  Cheers,
Steven in Jacksonville