Ok, I believe I have suggestions as to where bay placements would be:
Feel free to comment.
Notes: the spinal mount would be slightly sticking out of the forward bow of the ship.
Also, the missile system would be one big amount of missile silos clustered together: they would release swarms of capships (similar to the ones in BSG, wish smart homing capability (homing on a hostile while avoiding friendlies) but slower, as those missiles would be pry to interceptor/turret fire.
As far as turrets are concerned, I'm not that sure yet as turrets can mount quite different fighter armaments, but as a battleship, the ultor has maximum coverage. I have a photo here determining what might look like a standard leviathan turrets: It appears to have 4 cannons and 1 hard point for fighter class missile weaponry. it's on page 7 of the leviathan rulebook (the small domes on the ship surface).
as to quarters, it's a good idea: I believe though that the carriers are the ones suffering from that most (the xerxes for one, but perhaps the destroyer class carriers even more). Indeed, how they squeeze 144 fighters and the host of small ships on the canis destroyer class carrier is beyond me...

feedback awaited...
Edit: while I think of it, I won't be here for the next 2 weeks, so I'll be off the boards for a while. i hope no one gets bothered by that.
Best regards.
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