I think this is the key point. And I'll add a few more.
Whether you want a monotheistic cosmology or a monotheistic religion, you need to decide what you mean by monotheism.
A monotheistic cosmology, for instance, could easily have saints, demon lords, and celestial paragons who have every one of the abilities and powers ordinarily associated with D&D gods. So if you want a monotheistic cosmology, you need to decide what kind of scope both of action and abilities other entities have.
Similarly, a lot of people would consider a group of people who worship only one god to be monotheistic. Technically, this could be what is called henotheism where the worship of the one god does not deny the existence of other gods, but especially in a D&D style world with powerful demons, saints, etc there is a lot of overlap between the two concepts. A henotheist could easily maintain that his god is
better than the other gods--perhaps so much better that they're not really the same kind of being at all. Similarly, a monotheist might acknowledge powerful beings that influence life but are not worthy of worship.
Furthermore, I think Kahuna Burger is right on the mark when she suggests that the cosmology need not be transparent to the PCs or the denizens of the world. (Though making monotheistic societies work in a polytheistic cosmology when surrounded by polytheistic cultures is a bit of a challenge unless you reduce the monotheists to caricatures). Even if you have deities taking an active and visible role in the world, you can have quite a bit of ambiguity.
First, there are different levels of activity and visibility. For instance, let us say that Jupiter causes every lightning bolt to land where he throws it (sometimes, he is rather tipsy which is why it doesn't always fit a plan). That is a very active role in the world, and a quite visible one, but unless someone sees him throwing the bolts, it is, to the mass of humanity, indistinguishable from our own (presumably Jupiter free) world.
Similarly, we could give the priests of Tzizhet a large role in the administration of Myrantia. They lead the nation's worship and heal the peoples' ills (if properly bribed for their god's favor). They preserve the peoples' ancestors by animating them in the forms that fit their lives. In short, they provide innumerable demonstrations of magical power that they attribute to their god. But then they are visited by some travelers from Coryan who claim to recognize the worship of Tzizhet as a barbarous amalgamation of the rituals of two of their gods: Sarish and Neroth. This may be especially possible because Sarish is not the kind of god to ignore a properly conducted ritual just because someone got his name wrong. Now there are two competing interpretations of the cosmology (Tzizhet as an independent entity or Tzizhet as a label that ignorant barbarians apply to either Neroth, Sarish, or some partnership of the two) that are both possible based upon the extant evidence.
But let's say you want to go for full on forgotten realms style visibility and activity on the part of your deities. So, there is an especially successful orcish chieftain. Maybe he has divine blood and maybe he doesn't. But what's known certainly is that a monstrous one-eyed, horned figure appeared among his troops and tore down the gates of the Black Scar citadel when he besieged it. With his borders secured, he gathered all the local tribes and marched on the highlanders with this being in his van. The highland tribes opposed him at the Snake river and, as the great horned figure tore through their center, a glowing man with silver skin and feathered wing appeared bearing a golden bow. He smote the horned orc with his bow and pursued him into the clouds. Seeing what they interpreted as the avatar of their god turn tail, the orcs broke ranks and were ridden down by the highlanders. From that set of events, what is obvious? The Lord of the Golden Bow revered by the highlanders appeared. Old One Eye led the orcs to their defeat. That's probably how the orcs and the highlanders would see it. On the other hand, it's also possible that "Old One Eye" was just a balor summoned, as they sometimes are, by the vast number of sacrifices the orc chieftain made. (Or maybe, he was bound by the chief's lead shaman using an ancient scroll). Sure, he said that he was Gruumsch and the real gruumsch didn't strike him down, but maybe the real Gruumsch was busy at the time. Or maybe there is no real Gruumsch and Asmodeus sees fit to give the orc clerics spells because they accomplish evil on the earth. What about the Lord of the Golden Bow. Maybe that's who he is. Or maybe a Solar was able to travel to earth to oppose the demon because every incursion by devils into the mortal realm can be balanced. Or because Bahamut is the protector of humanity whether or not they worship him and wasn't about to let a demon lord wreak havoc on his people without interfering. The highlanders erected a fifty foot statue in honor of their deliverer on the orcish side of the snake river and offered sacrifices of thanksgiving before it. A great dragon--was it silver or was it white--appeared and smashed the statue, leaving a tablet of laws in its ruins. Was it because they were worshiping the servant of Bahamut rather than the god and they angered him? Did the Lord of the Golden Bow prefer the sacrifices of righteous living as defined in those tablets to sacrifices of horseflesh and grains? Did the dragon really leave a tablet of laws in the ruins of the statue? After all, it was the shaman MacGregor who found it and shaman MacGregor has done quite well for himself since uncovering it. And that bit about the tribes donating every twentieth horse to the shamans? Awfully convenient. Unless the creatues involved start delivering plot exposition, ordinary men and women in the world will find plenty of room for ambiguity as to the true divine order of the world. Add in a few bits of outright chicanery and some frauds (some of which are obviously punished by the gods and some of which aren't) and you have a lot of room for ambiguity.
Now a monotheistic cosmology both increases and decreases the opportunities for ambiguity. It can increase the ambiguity by erasing the distinction between a "god" and a demon prince, devil lord, or celestial paragon. Maybe none of them should be worshiped, but if they can all grant powers then how could ordinary mortals tell what they are? It can decrease the ambiguity because you probably don't have the "god x wasn't paying attention" or "god y was protecting the offender" excuses for what would otherwise be cosmology revealing events (for instance the balor from the previous example not being struck down instantly for impersonating Gruumsch--if that is indeed what happened). You also have to decide why the real god puts up with everything. Maybe he's giving the rebellious and deceptive mid-powered agents (the aforementioned demon princes, etc) time to change their minds rather than be destroyed. Maybe she regards humanity (and demi-humanity) as a failed experiment and just doesn't care. (Though in that case, you wonder why people worship her). Perhaps he's a social darwinist and wants to see people improve themselves through struggle. Perhaps he wants to give people a chance to follow voluntarily before starting with the compulsion. You could also just decide to leave that unexplained--perhaps tossing out three or four mutually exclusive options as positions advanced by the world's theologians.
It is actually not the activity or the visibility of the deities that makes the cosmology transparent in D&D books. What makes the cosmology of most D&D worlds transparent is the way it is presented in the setting books and the tendency of module writers and novelists to do divine plot exposition. On the other hand, where the setting information does not provide entirely transparent cosmology information such as the world of Arcanis, there is lots of room for ambiguity. In Arcanis, Henry Lopez probably knows whether Tzizhet is really Sarish, Neroth, both or neither, but the players don't. Similarly, Henry probably knows what Illir thinks of the emperor Calcestus and why he thinks that, and what his plans are, but the players have to guess based on information they discover in game.
In a homebrew setting, you can get some of that ambiguity by writing your descriptions empirically from the perspective of an inhabitant of the world. The mother church of Coryan teaches X. The Nierites of Erdukeen believe Y. The Myrantians believe Z. If some of X, Y, and Z is mutually exclusive, so much the better. You may not be able to keep the alignments of deities a secret if you want to preserve the "one step from deity's alignment" rule for clerics, but if you define the god's or various gods' teachings, and allow clerics to have alignments that fit with those teachings, it doesn't hurt the ambiguity too much. Players can figure out what alignment they think various teachings match anyway and there is always the possibility that the teachings and alignment are a trick.
Kahuna Burger said:
One very basic question I would ask is : Are you looking at a monotheistic religion, a monotheistic cosmology or both. A lot of the time we (ENworlders and fantasy gamers in general) seem to work under an assumption that cosmology will be accurately represented and understood in mortal religions. Working from the rules up, there's no particular reason for this. You could have philosophy clerics who believe they are channelling a non existant god, an arcane caster deliberately running a scam, devils giving splinter sects their powers, monotheistic religions who say that any other clerics get their powers from devils....
So I would consider both the mortal structure of religion and the cosmology that the PCs may someday come to understand.