i use blender too... 
well it looks like he made some new faces after he set the smoothing, just reselect and smooth again
Nope the auto smooth setting didn't like those faces, had to mess around with the wacked goemetry around the cockpit. If my original plans for this ship went right it'd be more of a destroyer now, but seeing as it looked to me

more like a fighter I changed it, and the cockpit addon wasn't done the best.
Edit: Updated the pic in my last post.
If your doing blocky FS2 type ships then yes, smoothing is really irrelevant. If your doing aerodynamic style, then smoothing is quite important, it'll allow you to get away with blockier ships than you would actually need. Personally this early on I'd remove smoothing all together.
Is this sorta what you were aiming for Davin?

Not quite, when I was modeling my ship I really couldn't visualize what I wanted clearly enough, and thats whats taken me the longest about making this thing. Just a question, how long did it take you to model that?
Anyways, good progress Davin. 
Out of curiosity, have you got a cockpit modeled under where I presume the glass is?
I really wish there was, I'll probably work on that thursday night, tommorrows a bit busy so i won't have any time to do work on it then. I was experimenting with glass materials with blender, and I wonder, If I did it in blender would it survive the conversion to cob? Because I personally loath ts 3.2