Altering zones and spheres is a tricky business, as i've been finding out recently myself.
There are no known 3D zone applications on general release, as yet.
Therefore to build a picture of where the zones and spheres are, means drawing boxes and spheres within a model, on a piece of paper, according to their co-ordinates in the .zon file, which can be opened, as Danilisa said, with skywaj's S3D editor.
Then you have to find out what those zones control, and how their alteration affects the reaction of the ship to damage.
There's no guide for that, it's trial and error.
Further down the SH3 mods workshop page is a thread entitled " Are there any free modelling applications"
You might find it useful.
