Like some of you here I've had this same idea ofmixing B5wars with the d20 game. I have experimented and i'll tell you what I did.
first, I scanned a Corprate Transport. I then used photoshop to do some editing of it. I removed all of the hitpoint boxes, weapon information and ship information as it related to the b5 wars stuff.
I left in place, however, all of the icons for weapons, thrusters, etc. Those that I left I gave 6 boxes that represented the 5 levels of critical hits, with the 6th box indicating that the object was destroyed.
I then put down the ships main hull HP as per D20 rules, and gave each of the 8 cargo pods their own seperate hit points as listed in the rules as well. The cargo ships DR is 8 so I listed that as well.
I left in place the hit location chart.
Now, imagine a Delta V attacking it on the port side. To make it simple the Raider hits the transport. The attacker rolls a d20 on the aft hits location (maybe the Delta V was left side but back more) and rolls a 9. He has struck cargo pod G. He does his damage. Next round.
Now, imagine if he had struck the ships particle canon. In this case I came up with a house rule. Take the damage the delta V (in this case) is doing the the transport and subtract it from the main hull of the ship, accounting for the DR. Now, divide this post-DR damage by the ships DR. This number is how many levels of critical the ships system took.
Eg: The raider hits and does 12 damage with 1st damage roll, and 10 with second damage roll. This rusults in 4dmg and 2dmg getting through DR. I would rule that the damage is stacked as the weapons both strike the same target (if I remember correctly from b5wars). So the total damage after DR is 6. Divide the damage by 8 and round up, to get 1. The particle canon takes 1 level of critical.
I think of it as the gun is what was struck, but that damage transfers to damge to the main hull as well.
I hope I was clear...this is my first post.