Thanks guys...I'm grateful for the assist.
I'm glad you popped your head in here D...I was starting to suspect you had more than a passing interest in "Trek" 🙂
So, here's the full story...
With the earlier attempts, yes...I used Booleans to cut the windows. This had a few pro's and con's. The upside is that as long as I didn't try to smooth or anything, yea...the render actually looked pretty decent with Maya software (as seen in my other thread on rendering). Likewise, the textures weren't too much of a headache either, as I was able to create the UV's based on the camera view. The down side however, is that I think this may be what has been wreaking havoc with Mentel Ray...when "good geometry goes bad".
So in exploring this, trying to get the best results visually with better geometry, I've been trying to explore some options...since this is for my own amusement more than anything, it's not like I'm on a deadline or anything, so I have some time to screw around with it.
Option 1 - skip trying to "cut" the windows and just do windows over the primary cylinder. It's "ok" and was fairly easy to do, however when I go to add the ambiant occlusion layer, it don't quite look right. Those windows really need to be cut and set into the hull.
Option 2 - yea...I was ahead of you guys here and cut some extra geometry into the hull then extruded the windows in. It's "better", however, the geometry (at this point at least) is still fairly messy...I'm honestly not sure if it's really THAT much better than the geometry from the Booleans (although I haven't tried any exports yet to test this theory). The problem of course is that trying to cut the geometry into the hull means having to deal with that taper. That said however, I did use the cut faces tool and was cutting across the WHOLE lower hull...ended up with a lot of tri's instead of quads. Looking at D's work there, I think I have a better idea (although suggestions are still quite welcome).
Now with that all said, here's an updated still using Option 2

Interestingly enough, this is actually a 3 layer render (not including the background), it's got a Maya Software layer, a Mental Ray layer and ambiant occlusion. I do think it's a fair sight better and, visually at least, moving in the right direction...but we're gonna be talking some MASSIVE render times if I try to go this route...at the moment I estimate the final animation is likely to be around 12.000 frames and so far, I haven't included the second ship or any planets or anything else...you get the idea.
Needless to say, once I hit post here, I'm gonna take yet ANOTHER crack at it...I think I've cut around 40 different versions of that hull during the little project.
Again thanks for the suggestions and a push in the right direction...please feel free to add more! 🙂