Select the verts, press e, move to wherever you want the bit to stick out to. Basic Blender modding technique.
Also, keep in mind that Blender has a lot more functionality than it appears. I've been using it for about 3-4 years now, and there are still new techniques and functions i find. My advice in that regard is to never assume blender doesn't have a certain function until you find proof that it doesn't.
As model advice, the power of blender comes from how easy it is to manipulate the mesh on a verticie by verticie basis. From what i can tell, you're barely using that power with this mesh.
Look into editing parts on a verticie level rather than manipulating primitive objects.
The next stage is to build ships practically face by face, or at least area by area. Once you get the hang of that, you'll find that any sort of details, shapes, greebles etc. are possible, and the whole model 'blends' (
) together far better than it otherwise would.
