Ultimately, when incorporating gods and religion into a game, you can do anything you like with it. Temple intrigue and politics, all out wars among the gods (thus their followers, i.e. "holy wars"/crusades), or simply a unifying presence that keeps its distance. It's entirely up to what you and your players want. Like a "heavy/light magic" or a "heavy/light rules system", whether or not you want your game "heavy or light on religion" is really your call.
I have long been fascinated and studied the various religions and mythologies of the ancient world. So forgive me, up front, for what is sure to be a lengthy post.
To answer your simple queries: when playing in an established setting, I'd use that setting's pantheon (FR, Greyhawk, someone else's homebrew). Most of the games of my youth were not in a setting and we were usually allowed to generate our own deities. I definitely prefer the pantheistic world view to a monotheistic one. It just makes things more mythological/magical/fantastic, for me.
The general attitude I wanted to create (and try to maintain) on Orea is that of the ancient world..."You worship the sun god named X. I worship the sun god called Y. They stand for (mostly) the same things and are essentially different names/faces for the same divine power. And we know and recognize that!" Or "Your god is my goddess' brother, so you and I should be as siblings." Pretty much, the only gods NOT tolerated are the cults of the real (chaotic) evil ones. But like any evil, you just can't keep 'em down. One or two gods of evil do even maintain public presences in some of Orea's larger cities.
My campaign setting of Orea has a lengthy creation mythology and a generation of "Elder gods" the bulk of whom were eventually overthrown (a la Greek) by their children, the current pantheon. The Elder gods (other than a chosen few) are banished from the realms and inaccessible for worship (...though rumors of secret cults trying to bring them back do arise from time to time
The current pantheon exists in. more or less, a balance (and you can get a breakdown on specifics here
http://www.enworld.org/forum/plots-places/294094-orea-redux-comments-questions-welcome.html ). The gods are NOT, generally, involved with the world first-hand. This was decreed by the king of the younger gods since their reason for overthrowing and banishing their predecessors was the Elder gods direct involvement which nearly decimated the world. Of course, certain evil gods are always looking to increase their power on the playground or "take over the world." But hey, that's what heroes are for!
The gods (greater and lesser) are divided as: 7 gods of Good (all mixed Lawful, Neutral and Chaotic), 7 gods of Evil (again Lawful, Neutral and Chaotic) and 8 Neutral gods (including True Neutrals, Lawful Neutral and Chaotic Neutrals) keeping things in creation moving. Within these are 1 Elder god of good (female), 2 Elder gods (one male, one female) of neutrality, and 1 Elder god of Evil (generally presumed male) who were allowed to remain within the planes accessible to Orea.
I slightly boosted the "side of good" because I want a heroic campaign/setting where characters are encouraged to be "the good guy". So I threw in minor 2 demi-gods (one LG and one NG. One is an actual "Sainted" mortal elevated to her station by her goddess and one is the traditional demi-god: son of a god and a mortal woman). So we have 9 divines powers (of varying levels) of Good.
Those are the gods that exist and rule over the realms of Orea.
A few of the larger/more powerful have differing names in differing regions. But ask any (human) farmer across Orea, "Who is the King of the Gods?" and he'll tell you "Astar, the Celestial Sovereign, of course." He will then go down the road and leave an offering at the outdoor altar to Sylari, goddess of nature and weather, for a good harvest in the fall.
While recognized the world over, certain gods have more "pull" in certain realms, based on their domains. Astar, is the most highly revered deity in the kingdom of Grinlia. As such, his temples hold much power throughout those realms. A sizable temple to him will be found in almost any city (and any LARGE city across all of Orea), abbeys and monasteries will be found spotting the countryside. But they are not a "dominating" religion. The temples of the other gods are left to go about their business (well, at least the good and neutral ones). Whereas in the wizard lands of R'Hath, the goddess of magic is the most powerful temple with the most followers. Though the other deities (including Astar) are paid tribute by those seeking their favor.
For non-human cultures, I generated limited pantheons (5-9 gods each) for elves, dwarves, gnomes, and halflings. They simply worship different aspects/faces/name of the same gods (and in the case of elves, some of the same names also).
RELIGION on the other hand, is a whole nuther' ball of wax.
Religion is a fabrication of culture. It is ritual, rite, defined by faith and dogma that is accepted (or rejected). I have incorporated all different types of religion into the world. From the larger, more established and power gods with large temple hierarchical structures to blood cults (god of pain) and secret sects (god of shadows, et al.) to shamans, some worshiping totem animals like the Gorunduu barbarian clans or nature spirits like the wild Kantiiri elves, some just worship anything that will give them power like the shamans and witch-doctors of the goblinoid tribes
To this blurb for what I decided about halfling religion:
"...While there is a "halfling pantheon" the only established "temple" with spell-casting clerics is the temple of Faerantha [the primary halfling goddess based on Yondalla] (though an outsider would find it difficult to tell a temple of Faerantha from any other cozy halfling dwelling.) the pantheon is worshiped as one, as a whole family in the same "house." The other deities are revered and sacrifices or prayers offered in adjoining shrines or individual family alters at home. An offering place on a mantle or small table in a side alcove with a likeness of Gaela [goddess of home and hearth], for example, can be found in almost any halfling abode."
As noted above (for example), the primary religion of Grinlia, is not the primary religion in R'Hath and neither is the primary of the south. But everyone acknowledges the same gods. Even in cultures where the names may be different, such as in the desert empire of Thelitia (though I kept this to a minimum for sanity's sake).
Druids, on Orea, are a separate ancient order that predates the current pantheon and does not worship any existing "god of man". Among the more "civilized" temples, druids are the "heathen." The druids' power, teaching and philosophies come from communion and immersion with primal energies of Orea itself. As such, members of the druidic order sometimes find themselves at odds with priests of the gods. Though, not surprisingly, the clerics of the nature goddess Sylari and the druids are often in agreement.
The druids, as an organization however tend not to concern themselves with the realms outside of their sacred woods and mounds. So conflict is minimal. Those wandering druids who take up residence near populated areas are generally welcomed and friendly with the local (rural) population.
So, in closing...decide how much and what kinds of religion/gods you want in the game world and...well...do what you want. lol.
There's my (ok, well, more than) 2 coppers.

--Steel Dragons