David Ackerman here. When I was asked by other authors about religion in the Southern Reaches, here are some of the thoughts I sent back. This is from a few years ago when concepts were still simple and details hazy, so things may have developed in different directions since then.
1. Magic exists independent of the Gods. Magic users in the Irwan Empire draw power directly from the universe and do not need a deity to act as an intermediary. You can be an Atheist and still throw spells.
2. The Gods can be real but shouldn't be TOO powerful, or, alternately, they aren't overly interested in directly interceding in this world. In fact, I'd even toyed with the idea that it's hard to be certain if the Gods are truly real or just collective magical constructs created by the minds and rituals of their worshipers. I just wanted to be careful: A bunch of vengeful Gods tromping around would make the Fae threat look rather pathetic. Many Mythic Histories of the World exist, but it is impossible to know which is really true. Most describe some sort of epic creation at the hands of deities who soon faded into the background or returned to their supernatural slumbers. They can still hear the prayers of the faithful, can act as magical 'batteries' for their agents (through blessing and spells), but are very rarely roused to direct action. Clerics and priests CAN draw power and spells from their Faith (whether real or constructed) and the churches do wield real social and political power under many circumstances, however.
3. The Fae feature heavily in almost every culture's myths, especially between 1500 and 10,000 years ago. They were the Godlings whose power and capriciousness warped the world, created many new beings, and made men cower in fear or bow in supplication. At the height of their reign, the other Gods interfered little or were even beaten back by the Fae's corporeal power. Illegal Fae cults still exist in many places and many have been carefully re-ignited since the return of the White Count.
4. Nature spirits and sentient magical entities DO exist. They may simply be elements of a magical ecology or lesser manifestations of a larger pantheon. Minor cults and faiths can certainly focus around them (panthestic river and forest spirits, etc.). The elves form alliances with many of these in something that looks like a religion but is really more of a complex set of mutually-beneficial rituals and minor sacrifices of POW. Croll may be a powerful variation of this.
5. The Imperial Faith was conceived as a religion based on the worship of the Irwan Imperial Family and its ancestors as well as a discrete set of 'approved' Gods (Kalar and Genio among them).