So here's a neat trick to make weapons look like they're sticking out of the sides of sections: Make a section big enough to cover most of the gun except for the end or tip of it. Then, make a child section that is smaller than that section, and obscure it underneath the first section. Then, add a weapon to the obscured section, hitting W to put it at the same layer. Now just move the gun around until it sticks out of the top layer the way you want.
I made a screen shot that shows the result on a ship I made:

Maybe this idea was immediately obvious to a lot of you. I dunno. But just in case it wasn't, I thought I'd post it.