I figure since these things will be expensive and huge there are going to be relatively few of them meaning their main use will be firing at the ground. For that reason I would go for a more zeppeliny look with turrets and bomb bays on the bottom kind of like the Goliath from Castle In The Sky minus all the helicopter blades.
I also think having smaller ships docked onto it would be usefull for recon and look really cool.
Anyway, thats my two cents but good luck with your writing.