One thing that really bugs me in many settings is the pantheon of gods idea where you have a section in the setting book about all the gods the clerics can select from. Gods like Chauncey: God of Light Transport, and Swee-tah: Goddess of Those Who Died from Poor Dental Hygiene. Don't get me wrong - I love things like the Street of the Gods in Lankhmar, but in a campaign it doesn't work for me unless the different clerics had play differences and/or unique powers - or if there were no clerics. That being said, I think for setting materials I will be going with a single church model. A single model doesn't mean that all the clerics are of one mind or on the same sides - I would certainly expect factions or even different orders within this church. I don't think that the concept of a personal (even chatty) relationship with a Deity is the right one for this model because having a very aware and communicative God would have too much impact on the world. If a God was to take part and speak plain and direct to their flock like this, the world would become something more like a game of Populous or Civilization. Leave a little mystery I say.
I'm going with something like... the Lords of Order. Who are they? Well they carved the world out of Chaos. What are they? We don't really know. What do they want? They want to keep Chaos at bay. What is Chaos? That's what exists outside the world, from before the world - that's where Demons come from. Are they good and just or cunning and evil? Well um... both - that's why we cure and heal people and worship them but also that's why there are devils and suffering and injustice. Why both - because both might and mercy are required to establish order. Do we have free will to choose? Yes you can choose to be good and merciful or mighty and evil, however both good and evil must be opposed to the destruction of chaos. Is the Church good or evil? The church strives to spread mercy, might needs no help to spread. How many Lords of Order are there? We don't know. How do they grant you special powers? We don't know, they choose people some for mercy, some for valor, some to smite chaos and some for reasons we don't understand. Do demons also grant special powers? Yes to some - those are cults and they need to be stopped from bringing chaos upon us.
Some of the 'Lords of Order' are going to be Godly and angelic beings, however some are just as obviously going to be Devils and Lords of Hell. All beings of Order have their place in their hierarchy and abide by rules when dealing with people and each other. A devil can't corrupt a soul by force and won't forswear themselves even if they will try to trick or intimidate a character. On the other hand, demons are just in it for the destruction and have no problem with creating undead or possessing characters or going back on their word.
So one church and yes, I'm sure GM's and players will invent doctrine and saints to follow or invest particular attributes to certain Lords of Order to make things interesting. Given that you have a church that can actually grant miracles, it will be assumed that they are very influential socially and the only thing stopping them from being the major force in society is this ambiguous theology, well that and the three way struggle between mercy-might and chaos.
This goes back to an old school small scale vibe where you have the forces of Chaos nibbling at the periphery of society in the form of goblin bands and mad cultists and horrible demons - and the adventurers are going in and stomping them down. No alignments in Beacon so players can play selfless paragons just as easily as opportunist swords-for-hire. They are all skulls for the skull throne.