Sledgehammer the zones ARE individual compartments within the model, that's what the zone co-ordinates define( X,Y and Z). 3D boxes.
The zones define certain vital areas within the model, such as the number of engine rooms and their dimensions, fuel and ammo bunker dimensions.
The compartments (zones) contain their own armour levels, and a gun shell of a given size is assigned a certain destructive power. If it's a big shell with enough power to penetrate both the hull armour, and the armour for the internal zone, engine rooms flood, ammo/fuel bunkers explode etc.
The models tendency to list, due to taking on water, and ultimately sink, is determined by the strength of the hull armour, plus the level of "flotability" assigned to various compartments (zones) within the model, sometimes seperate from, but often in combination with, the afforementioned areas being penetrated (fuel/ammo/engine zones).
But flotability zones are seperate from those areas, and as such have their own dedicated dimensions and settings.
When an important, or critical, area is penetrated by gunfire, bomb or torpedo, it can also trigger a sphere to activate.
The spheres are 3 dimensional cylindrical areas, with various radii ( radiuses

), which, when penetrated, produce effects, like explosions, smoke and fire. These are normally linked to the important/critical zones.
( Lots of penetration occuring here

)
I get the sneaky feeling that you already know this

but just in case, that's a laymans description of how the ships behaviour, and the effects, are determined

.
Bottom line is that the zones and spheres are indeed individual compartments, that already exist within the model to determine it's behaviour.
karamazovnew i looked up the free version of maya, but it no longer appears to exist on their site ( or at least i couldn't find it).
So far i've got Misfit, Blender and Gimp, and with Sledgehammers help i can now view the model in 3D through Misfit, but still can't view the zones (yet). But their must be a way, i just gotta find it.
Edit:
Karamazovnew i went to Autodesk via a search link, that i think put me on the wrong page.
Just searched it again and there's a 30 day free trial version of maya on it.