The necessity of working out the metaphysics and mechanics of gods is actually one of the reasons I've delayed on the Auran Empire campaign setting. It's something I've given a lot of thought to. Here's my current thoughts, susceptible to change.
At present, my interpretation is that existence is defined by the interaction of the Pneuma* (the creative force or cosmic soul) and the Logos (the laws which govern the expression of the Pneuma). The Pneuma created the Logos but in the process bound itself into every expression of the Logos. As such all things possess a fragment of the Pneuma within themselves - said fragment being called its soul.
The ability of physical matter to host a soul is dependent on its configuration and properties - its form in classical parlance. Death results when the physical form becomes so damaged or decrepit that it can no longer contain a complete soul. When this occurs, the soul transmigrates to a new form which can contain it. This process is called reincarnation or metempsychosis. Complete reincarnation does not occur immediately, however. When a living creature dies, a residue of its soul may remain coagulate within the body for a time, only gradually dissipating from its corpse. It is this residue of the soul that a spellcaster speaks with when using speak with dead. And it is this residue of the soul that makes the organs and blood of creatures valuable as special components. How much of a residual soul remains depends on many factors. How intact is the body? The more intact the body, the more residue of the soul will remain. How powerful was the deceased? More powerful souls tend to linger longer. What is the alignment of the spheres of existence? The more distant the outer spheres, the longer a soul will linger. How long has the creature been dead? The more time has elapsed, the less divine power will remain.
In game terms, the total amount of divine power possessed by a creature is equal to ten times its XP value. When a creature dies, about 90% of this value typically transmigrates very rapidly; the other 10% remains as a residue within the creature’s blood or organs, which can be harvested as special components for magical research. When a creature is sacrificed, 80% of its divine power passes to the entity worshipped, 10% is retained by the sacrificer for his own ends, and 10% remains residual within its blood and organs. This is why divine power why XP value = special component value = sacrifice value.
A living creature sustains its soul through the biological processes of its living form. It bleeds off excess divine power each day equal to 6% of its XP value. Casters use some of this to fuel their spells but the rest is dissipated or bequeathed to a god through worship. A cleric that leads a congregant in worship collects about 10% while the god collects the rest – which is why 50 0-level congregants (worth 5xp each) generate (5 x 50 x 6% x 10% x 7) 10gp worth of divine power for their cleric.
The definition of a living creature, in fact, is one that sustains its soul through the biological processes of its body. The definition of an undead creature is one that sustains its soul through feeding on the souls of the living. This can be through feeding on spiritual residue found in corpses (as a ghoul) or from directly draining the life energy of living creatures (like a wraith or vampire).
Following from this, the definition of a god is a living being that sustains its soul through divine worship and sacrifice.
A note on the spheres: In the Auran Empire setting, the various spheres of existence (Chthonic Darkness, Empyrean Heaven, and the Elemental Planes) are all coterminous simulacra of the primary sphere (akin to the Shadowfell and Feywild in 4E/5E D&D, or to the Ethereal in 1E/2E). The geography of the world is mirrored in the geography of the other spheres, albeit in a distorted format representative of the nature of the other sphere. Thus the Empyrean gods could be said to live on the peak of Mt. Audarammas, but the Mt. Audarammas they live on is in the Empyrean Heaven.
The spheres are always in motion. When an other sphere is are juxtaposed with the primary sphere, it becomes possible to pass between at various gateways. Thus on certain high holy days, when the spheres are aligned, one might pass from Mt. Audarammas on the primary sphere to Mt. Audarammas on the Empyrean Heaven.
*Pneuma is very much the *correct* word in terms of the Stoic origins of this concept but it seems like it sounds wrong to modern English ears. I'm open to suggestions of an alternative. Numen? Numina? The Divine? Psychocosm? Cosmic Soul? Oversoul?