I'm gonna have to agree with mhacdebhandia. The best way to handle religion is to get rid of the gods.
The various fantasy rpgs, novels, and video games I've seen all have an interconnected pantheon, in that the followers of each god belive in the other gods as well. That reflects poorly the medieval era that fantasy draws much of it's flavor from.
Set up three or four seperate belief systems, then decide how they interact. Below is an off-the-top-of-my-head example:
In the beginning, the three chaoses spawned the titan Imeros. But his children, the seven high-gods, rose up and killed him, creating the world from his bones, and it's creatures from his flesh. They and their children, the ninty-nine lesser gods, each have power over some aspect of reality. A god can grant its followers some small segment of its power, thereby creating clerics and paladins. But there is also power in the titan Imeros and the three chaoses. Rangers and Druids listen to the voice of Imeros, and gain power from his wisdom. Others impose order upon chaos through various means. Some do it with rituals and diagrams, becoming wizards. Some do it with music, becoming bards. And some, the mysterious sorcerors, do it with will alone.
In the beginning, there was vast emptiness. Then, a light came into being. A light known as Luminus. Luminus shaped the world and everything within. To his chosen, he granted great powers: his pious warriors became paladins, his mortal servants became clerics, and a blessed few were favored at birth with the powers of a sorcerer. But where there is light, there are shadows. Nocture, the enemy of Luminus seeks ever to destroy all of creation. And in his attempt to do so, he has created vile corruptions of Luminus' chosen. Wizards seek to do with twisted speech and vile geometry what sorcerers do by nature of their birth. Bards gain powers through revelry and debauchery that paladins gain through prayer and meditation. And his devoted slaves have been granted their own clerical powers. Between Light and darkness is the realm of nature. Nature has magic of its own, and Rangers and Druids can access that magic, for good or ill.
In the beginning, there were countless spirits. And the spirits clothed themselves in forms, becoming the rocks, the trees, the rivers, the winds, the birds, the beasts, and even the people of the world. And those spirits continue to thrive. Rangers and Druids speak to the various spirits, and so gain their powers. Clerics and Paladins have entered into a relationship with a specific powerful spirit. Wizards deal with the spirits of Aether, Bards with the spirits of music, and Sorcerors with spirits within themselves.
In the beginning, there was man. He needs no gods or spirits to rule or keep the world in operation, for power lies always within. Belief is a power from within. Clerics, Druids, Paladins, and Rangers all derive their abilities from belief. Wizards, on the other hand, gain power through knowledge, Bards gain power through imagination, and Sorcerers Gain power through Will alone.
As set up, the classes always derive there magical powers and abilities the same way, but the interpretation is different. For example, rangers and druids all gain their their powers from mystic whisperings of nature, but some believe those are whisperings of Imeros, others that they are echoes of Luminus or Nocturne. Still others believe that the whispers are the voices of spirits, and finally, some believe that the whispers are a manifestation of our subconcious.
How do these guys get along?
The Polytheists get along well with the Spiritualists. Essentially, they believe that the so called spirits are simply the gods and their servants by different names. They don't have a lot of respect for the Atheists, but leave it to the gods to correct their irreverence and hubris. They actively war against the Monotheists, for clearly they pay reverence to a false god who seeks to topple the true pantheon.
The Monotheists don't much like the Polytheists and the Spiritualists. Clearly, these false gods and spirits are ruses perpetrated by Nocturne and his devilish minions. They're more lenient with the Atheists, however. For while the Atheists refuse worship to Luminus, they refuse service to Nocturne, too.
The Spiritualists get along well with the Polytheists, whom they consider odd for paying homage only to the more prominent spirits. They would likewise behave towards the Monotheists, except that the Monotheists have no intention of cooperation. They also don't deal well with the Atheists, who pay no respect to the spirits, and should be taught a stern lesson.
The Atheists find all of the others to be silly and superstitious, but don't try to make an issue out of religious differences. Unfortunatly, the Spiritualists DO make an issue out of religious differences, which has some unfortunate (and somewhat bloody) consequences. They get along better with the Monotheists (and to a lesser extend, the Polytheists)
