That's really too big a subject for me to resolve in a single article, but I can give you a checklist of stuff you need. If you want more I have two resources to recommend to you:
Wikipedia is good not so much for giving you a detailed description of the Babylonian, Roman, Greek, Egyptian etc religion. Rather it gives you clues about where to look for more information.
If you got GURPS Religion you might still benefit from the checklist I'll run through.
Also see: Part I and Part III
1. What's your society like?
Generally the gods you worship depends somewhat on what your society is like, or more accurately what your society was like when you first got your gods.
That said your society isn't necessarily as important when it comes to the gods as when it comes to priests and temples. In other words your society shapes the organised religion that occurs inside of it.
The more organised a state is the more organised the religious practises will be. Even if your mythology and pantheon has remained unchanged for centuries. Unless of course the gods demand/are offended by a high level of organisation.
At some point each city may have a united clergy, e.g. all the priests of recognised state supported cults are working for the same organisation, and recognise the same head; like the Pontifex Maximus.
If you want still more organisation you need a unified nation that shares roughly the same gods and mythology, and you need it to stay united for a long time. When that happens you may have an entire country united under one religious hierarchy. Ancient Egypt is the best example here, where Memphis was the religious capital, and the Pharaoh was also the high-priest.
However even the power of Memphis ended at the borders of Egypt.
There were no examples of massive religious hierarchies that crossed national borders, even if they shared the same basic mythology.
If you wonder why the answer is simple enough: Why should we ask the gods to protect and help those bastards over there? We want the gods to help us! To be nice to us! That lot over there can take care of themselves, and if not, tough!
Religious practise is always based around the community, and the benefit of the community. In such an environment there's no room for, or need of, a Catholic Church with more gods.
2. What gods are there?
Have you ever said, or heard someone say, something like this:
"Uhm... okay I got Pilfericus the god of thiefs, Screechicus the god of music and bards, and Hocuspocus the god of magic, and Hackoslashus the god of war, and Firstaidicus god of healing, and, uhm, Farmicus for farms, and agriculture, and all that stuff."
Better yet there really isn't anything that binds this lot together? They're just a bunch of gods with weird names and various portfolios?
In the next few sections we'll get to linking the gods together, but let's take the list of gods first...
How many Roman gods had pastoral or agricultural aspects? Let's see: Janus, Saturn, Ops, Consus, Ceres, Dionysus, Silvanus, Pales, Vertumnus, Pomona, and Felicitas. There are gods of pasture land, of cereals, of wines, and so forth and so on. I could make a list of gods and goddesses involved with fertility, and it'd be equally long.
Things like war, travel, fortune, the sea, had one to four gods related to them, though generally these were mainly in the hands of one or two gods. Meanwhile agriculture and fertility has what? A dozen gods each, of which at least four are fairly important?
You can definitely see what the Roman priorities were; agriculture and fertility were so important that you couldn't leave anything to chance. In fact that was pretty much the attitude of all ancient peoples.
Incidentally a people who live by fishing or silviculture will probably have a lot of gods for that as well. Whatever you do to get the next meal will be important enough to have a god linked to it.
You may have noticed that there seems to be a bit of overlap here, for instance Janus is also the god of doorways. This is true; many gods had multiple charges, some of which clashed with those of other gods. Generally the ancient Pagans solved that problem by worshipping all the relevant gods, but paying more attention to the big ones. At any rate it was no big deal.
So don't be afraid to be messy! You don't have to assign duties to your gods like a head of state assigns them to the members of his cabinet!
Speaking of heads of state, while you're at it you should consider if your Kings or Emperors are considered literally divine, or if they're thought to become deities after death. You should also ask yourself whether it's true or not.
How you answer that question will have big ramifications on your religious system, and how the gods interact with mortals.
3. The Creation Story
All cultures that I've encountered have one or more of those, sometimes multiple creation stories contradict each other, and sometimes they don't. If you've read Part I you'll know why most ancient people won't be too worried about conflicting creation stories.
So what does a good creation story, or stories, have to cover? Well there's three basic points:
The exact order varies a lot, and it can often get very involved. As an example I give you the Greek Creation Myth and the Norse Creation Myth. These are of course fairly abbreviated versions, but it shouldn't be hard to find the complete versions online.
At this point you may be scratching your head and going, "But wait, what's the moral of the story?" That's easy to answer: There isn't one.
Notice how none of the creation stories I listed had a moral, and indeed most creation stories have no moral. In my opinion the greatest weakness of many fictional Creation Myths, is the attempt to insert a moral into them. There really is no need, and it makes the story sound hokey.
That doesn't mean that there's no point to the stories, there is a point to them. First they explain how the world, the god(s), and humans came to be, that's three points right there. There may be secondary points such as: Odin is the King of the gods; or Ahura Mazda created everything, and therefore he alone should be worshipped.
Moreover the story tellers of old rarely go "Oh how terrible was the doom of Whatever" when they tell a story. They just tell the story without passing judgement on it. If someone does something bad in it they assume that the listener has enough wits to realise that this is a bad thing.
4. The Wicked Humans Are Punished (Optional)
This point is optional, not all mythologies has it, but it's fairly common.
Wicked Humans Are Punished (WHAP) stories are popular in places where:
Any one point will do the trick, the Aztecs had all three, the Egyptians and the Babylonians had one or two. All of them had WHAP stories. The reasons behind the WHAP stories varies, but generally the people had grown greedy, impious, and dishonest. In short all the bad things that could lead to the downfall of society, and which people have been griping about since time immemorial.
Outright rebellion against the gods is rarer, but in Egyptian myth the humans rebelled against Ra. Yes that's from actual myth, and not from Stargate.
It goes something like this: Seeing that Ra seemed to have lost his grip on things, rebelled against him. As a result Ra sent his daughter Sekhmet (or had the goddesses Hathor and Sekhmet combine into Hathor-Sekhmet) to Earth to slaughter the disobedient humans.
So humanity got whupped by the goddess of love and beauty, which I must say is somewhat novel...
By comparison the Aztecs list is fairly normal: the first age ended with the people being eaten by jaguars; the second ended due to a great wind; the third due to fire; and the fourth ended with a flood.
Of those four fire and floods are the most common in WHAP stories. Indeed flood stories are very common, even among widely separated cultures. Often a single person is warned beforehand and builds a boat, so he and his family survives while the rest of the world drowns.
Some people say this is because early civilizations build in flood plains, others that it's an ancestral memory of an actual flood. Take your pick.
Generally WHAP stories involve whatever the locals think is most threatening, and so the Aztecs get jaguars, hurricanes, floods and so forth. The Babylonians get floods, and the Egyptians get berserker love goddesses.
Would you believe that ancient peoples thought Egypt was weird? It's true! The ancients viewed Egypt like we view Japan; lots of really awesome stuff, but very freaky.
Alright, so I said this was optional, the Greco-Roman mythology and the Norse mythology has no WHAP stories. Or to be precise they have no stories of collective punishment; individual humans may be afflicted, but not humanity as a whole.
I'll qualify that briefly, the Greeks did have a story that Atlantis sunk because Poseidon was offended by the impiety of the Atlanteans. However this myth doesn't seem to be all that central to their mythology, indeed moderns probably think more about Atlantis than the ancient Greeks ever did.
The Greeks also believed that before this, the Iron Age, there'd been a Golden Age, a Silver Age, a Bronze Age, and a Heroic Age. Each successively baser than the previous one. Such beliefs are fairly common, in fact the first city dwellers thousands of years ago complained of how complicated life was nowadays, compared to the simple and virtuous past.
However such Golden Ages didn't necessarily fall because of greed, impiety etc, it could be just a natural calamity.
5. Who are the gods?
"Uhm, Hackoslashus is very strong, and, ah, uh, he doesn't like Hocuspocus 'cause you know magic is sneaky."
Your gods should not be reducible to their portfolio, if your god of war is indistinguishable from any cardboard barbarian, you should reconsider.
For instance why would a god of war be against magic? If he's the god of war, and not the god of Honourable Single Combats Where Everyone Plays Fair then why is he acting like this?
Why can't the god of war be brave and a stout fighter, but also treacherous and conniving, someone who'll finish the fight quickly? Why can't the god of thieves also be the god of the merchants the thieves steal from (Hermes).
Another thing that is often missing from many fictional pantheons is the king of the gods; the Greco-Romans had Zeus or Jupiter, the Norse has Odin, the Egyptians had Ra. Who is in charge of the Munchkinous pantheon?
Incidentally I'm talking about the king of gods, not the god of gods, having a being that the gods worship doth not a king make.
In real mythologies the gods often have relatives; parents, spouses, even children. This is, as far as I can tell, almost unheard of in fictional mythologies. I can't imagine why though, unless it's a result of the same lack of imagination I see elsewhere.
Here's a few ideas:
I'm sure you can think of your own ideas!
Once you got their personalities down, and perhaps a few areas of conflict, you can start writing your own mythology. Here I have good news: Don't worry if your stories are a bit bizarre, and resemble a mixture of action movies, divine soap opera, and sit com. That's pretty much par for the course.
So don't be afraid to have your gods do stupid things, or screw up, but generally they should get things right in the end.
6. Beyond Good and Evil
Simply put most Pagan gods aren't nice. Sure there are exceptions, like the Egyptian pantheon (though they can be pretty nasty at times), and some gods are more helpful than others. However when it comes right down to it the gods are powerful beings in a world that doesn't suffer fools or weaklings.
They act accordingly.
You will not find Lawful Good deities in most real world mythologies, and even fewer that act according to the Code of the Honourable Barbarian. Thor, the very picture of the Honourable Barbarian, once disguised himself as Freya to recover his hammer (read it here).
Certainly Thor was true to his word, protected men from trolls and Jotuns, and was a very popular god. However he was no fool, he would act "dishonourably" if the circumstances demanded it. So would pretty much all of the Norse gods, they were a fairly pragmatic lot.
Look at the Greco-Roman gods and how they treat people who cross them! If you're lucky you get torn to pieces by wild dogs, or transformed into a woodpecker.
Yet there's not a single God of Evil among them, and why is that?
It could be that the concept of evil simply doesn't exist in many cultures. Neither does the idea of sin for that matter. Even so there are sometimes acts that make you ritually unclean, and there are always some other acts that are considered wrong, or dishonourable.
Even those cultures that do have a concept of evil wouldn't necessarily reject gods that are affiliated with evil or negative forces. For instance Set, who many people think of as the stereotypical evil god, was openly worshipped throughout the pagan era In Egypt. The reason is twofold, first he had a positive side as well, and second you'd want to appease such a powerful god.
So even if you have a dark and savage god there's no need to hide his temple In the Gulley of Ultimate Darkness From Which No Man Has Returned! It can be on the main street, attended by perfectly respectable people.
Anyway I'll stop here, but later I may write a brief note about rituals.