Hi Brian,
To clarify, because it took me ages to work this out:
Working on the interior editor does, as you say, put in the system but not the "barrel".
If a hit passes through your shields, it will damage whatever system is nearest that part of the mesh on the .snt file.
To put in the barrel, you have to use the yellow line/cross system on the exterior view. Move it with the W,A,S,D. Make a note of the x,y,z coordinates and put those into the <vessel> entry for your custom ship in the vesseldata.xml file. This is the point on the mesh that the beam comes out of and sets the middle of the firing arc too.
Also, if you want to do beams on the rear of your ship, hold the W key until the yellow line flips all the way over. You can't get to the rear of the ship via the A and D keys.
A and B I think are place holders.
I'd really love for Thom to release some more info on using the ship editor. It is billed as a rough and ready app, but it's all we have and is quite frustrating to try to use.
"We should give him the send-off he deserves. He died saving us all. Prepare a Rocket-Shed for immediate launch."