Steve,
What does it look like when 9 pt two missiles hit two columns apart?
First Hit
00.....0000
000...00000
0000.000000
-----------
Second hit - if any of the template hits armor, stop on first row
00.......00
000.....000
0000.0.0000
-----------
or
Second hit - RL stype - Begin damage template where the center hits first armor
00.....0000
000......00
0000....000
------x----
Or, is it something else?
Something else. Think of the damage as little stacks of 1pt damage blocks in each column that are not connected to adjacent columns. In other words, if a 2-pt missile (adjacent damage blocks) hits a pit in the armor (say from a laser strike) that is 1 column wide and 3 deep, the point over the pit will do damage to layer 4, while the point that's hitting "fresh" armore will do damage to layer one. To put it another way, armor can never be damaged in such a way that there's an "overhang" (as in your last example).
So the answer to your question is:
00.......00
000.....000
0000...0000
----xxx-----
Think of it another way: Missile 1 does damage of 1232100 to the columns affected. Missile 2 does damage of 0012321. Add these together and get 1244421. For armor 3, that means 3 points penetrate.
John