This can get complicated, fast.
So here goes, and the best way to do this is by example.
Start with 3 CAs, each of them has 16 hull boxes.
Fed CA allocates them 12 Forward, 4 Aft
ISC CA (Or Lyran Tiger CA) allocates them 8 Forward, 8 Aft
Gorn CA allocates them 4 Forward, 4 Aft, and 8 Center
Now, let's simplify the damage allocations. Let's say that Forward Hull protects weapons, and Aft hull protects engines. It's a generalization, there are a lot more things to be hit between the hull and the weapons / engines.
And so, each ship gets hit with 20 damage, for single internals. Oddly enough, they alternate, in order, between Forward and Aft hull hits...
In the end, the Fed gets it "lucky". 10 forward hits wipe out 10 of 12 forward hull. Of the 10 rear hits, 4 knock out hull, and 6 blow up engines.
The ISC / Lyrans are okay, they lost all their hull, and a pair of weapons and 2 points of power. Being they gave up Ph-3s, the ship isn't too bad off.
The Gorn
could come out of it like the Lyrans / ISC. They could use up the forward and aft hull first (for 8 total hits), then 8 more to center hull (as the next 8 hull hits have to come off of center hull) finishes off the Gorn hull, leaving the last 4 damage to split between weapons and power. Or, they could decide to "protect" the engines. The first Forward hit goes to F-hull, while the first Rear hit goes to C-hull. After 8 hits, he's out of F-hull, lost 4 of his 8 C-hull, and no R-hull. Since all remaining F-hull hits come off the center hull now, he allocates his damage like this: 2 Forward hits on F-Hull, 2 Aft hits on Center hull, finishing it off. With 12 of the 20 damage gone, and no more Forward Hull hits, the ship takes some damage. The last 4 FH hits kill weapons, while the last 4 Aft hits knock out the regular rear hull, leaving the gorn down a few weapons, but with his engines completely intact, so he can outrun the incoming seeking weapons...
In the end, the order can be whatever they want...
Meanwhile, on the ships that are purely C-hull, it's another story. All F-hull and A-hull hits have to allocate to C-hull. So, taking a ship like the Hydran CAs with 21 C-hull, the first 21 hull hits of any kind go to that center hull, but once it's gone, then the whole ship starts to fall apart, as everything (weapons and power) is exposed.