I've commented previously on how Midnight benefits from heretical legates. Since this is rapidly becoming relevant to my current game, and one of my PCs has Theology, here's the data dump.
Structure of the church: The church is currently fragmented and disorganized. There used to be a Speaker for Darkness, whose word was divine law, but Naxander the Conqueror killed it and received the Dark God's blessing. When he died, he did not leave a clear successor for the position, and now the princes each vie not only for temporal power but also the support of the church factions, hoping to be acknowledged as the Speaker. Some legate factions support the princes, while others believe that the next Speaker must come from the ranks of the legates themselves. A few believe that the Speakership is permanently lost. It is commonly believed that pilgrimage to the City of Black Ice is a requirement for Speakership; currently the City is held by a militant brotherhood of legates, but should a prince take the city (despite the logistical difficulties), that would greatly contribute to the legitimacy of their claim to Speakership.
Monolithicity: The orthodox position is that the Shadow is the only Shadow and brooks the worship of no other gods. However, many of the primitive far-northern tribes that Naxander the Conqueror led out of the north have attributed deific status to him, in their tradition of ancestor-worship. These "dualist" sects claim witnesses to miracles surrounding Naxander's death as support for this belief. Some trinitarian orc sects even claim there are three divinities - the Shadow, the Conqueror, and an orcish messiah yet to come.
The End of Days: Most orthodox "accelerationist" human sects hold that when the Shadow has devoured everything, it will break the interplanar veil and release the trapped souls of the dead to afterlives of its choosing. It follows then that acts in service of the Shadow (sacrificing all the mans, absorbing all the magic items) accelerate this process, and bringing about the End as quickly as possible is a good thing because it will put the spirits of the dead at peace. Some scholastic, gradualist sects, however, believe that intelligent life converts "potential" trapped in the land itself into harvestable energy, and question whether or not just sacrificing all life would provide enough energy to shatter the Veil. These sects promote fertility and economic investments aimed at producing large, stable populations, with the intent of guaranteeing the End eventually after depleting all of the residual magic of the soil and sun (a process accelerated by having more people). Many gradualist heretics have found favor with the Princes, as sacrificing all the peasants weakens the army and leads to being crushed by one's rivals. Finally, orcish variants of the End of Days include "we kill all the humans and reign over this, our destined dominion" and "we kill all the humans and the Shadow transports us, Its chosen people, to some other world to conquer and despoil in Its name."
Divine Revelation: Some orthodox sects accept only the recorded words of the Speakers as canon ("Canonists"), while others believe that the Shadow grants divine revelation to chosen prophets beyond the Speaker ("Revelationists") or anyone at all ("Individualists"). This leads to any number of contentious minor theological differences (whether you can eat fish on wednesdays, the type of dagger appropriate for sacrificing halflings, and so forth) depending on which version of the canon you're using.
For its part, the Shadow doesn't seem to care much about any of these matters; everyone still gets the same number of spells per day. On the other hand, perhaps it is just testing its followers, weeding out the weak. The joy and terror of evil gods is that sometimes they're just messing with you.
A few sample sects:
The Militant Brotherhood of the Monolith: Guardians of the City of Black Ice, super-orthodox. Currently backing no candidate for Speaker (believe it will be obvious when the Shadow chooses, all current claimants therefore impostors), violently monotheist accelerationist canonists.
The Whisperers: Cultists who spread the worship of darkness in human lands before Naxander came. When he did, they came out of the woodwork and set up shop in places where they already had influence. Often cooperate with other Whisperer organizations in neighboring towns, tend to have a established political bases. The shrine legates in Ostergot are of this faction. Typically believe that the next Speaker must be a legate (and question Naxander's claim to Speakership), belligerently monotheist, moderate to lip-service accelerationist, and belligerently revelationist.
The Skami: A collective term for the tribes that Naxander brought south, the Skami have formed a sort of priestly class in many of the large cities that they conquered. They are often in conflict with their local Whisperer organizations for power; while the Whisperers have economic / peasant support, the Skami can draw on their settled tribal warriors. They usually favor either their local Prince or a powerful Skami kinsman for Speakership, are mostly dualists, lean pragmatically gradualist (gradualism offers many fruits for the decadent priest-nobility as well as the favor of the Prince, but they typically don't really grok the metaphysical arguments about gaian potential and the Veil, and sometimes it's politically useful to sacrifice a bunch of those Whisperer-loyal peasants), and are also often pragmatically revelationist. The Skami are weak in the Vale of Traitors, as the region maintained much of its own native nobility and autonomy, but are strong in Verlath the dragon's realm, where their tribes displaced or enslaved many of the Norse natives.
The Scholastics: While the Whisperers got their start via the Shadow's whispers and messengers, the Scholastics began as wizards who experimented too greedily and too deep, and glimpsed the coming darkness with prophetic certainty. Though few in number and often considered illegitimate by other legate branches, they do get spells and turning, and those sufficiently politically adept often hold high favor with the Princes. No consensus on Speakership, monotheist gradualist individualists. May warrant a custom class or something (because to be honest, these are the guys the PCs are going to want to ally with and henchrecruit, and also the ones who make the least sense in plate).
The Udareen: The orcish holy women hold beliefs just as heretical as the Scholastics, but have an army to back them up. Believe that orcs are the Chosen People; the next Speaker will be an orc, trinitarian accelerationist (with favorable orc End of Days) individualists (but divine revelations by non-orcs are invalid). Tolerated by non-orc Princes who value their hordes, a common enemy for the other legate factions.