Sorry this got a bit wordy but the concepts aren't as complex as the length might make it appear. Please feel free to add your own ideas as well. I know I haven't thought of everything.
![Very Happy :D](./images/smilies/icon_e_biggrin.gif)
1. Simplicity: Don't go overboard on making things complex. You can add most of these sorts of things in later if you need although if you have a very rough sketch at the start (maybe a paragraph to describe the whole setup; see the examples below) that also has advantages. You can build layers and add complexity as you go if you aren't sure what to do right away. Putting it off actually lets you make these extra layers have more to do with the PCs and their actions. Doing it all before the game starts allows you to tie the different plots together better. It's a trade-off.
2. Three: I've found that if you have three active plots going at once, your players start to assume that the whole world is slowly moving under their feet. The first one is your obvious plot when the game starts if you have one. You can hide this a little so the players only really clue in after 2 or 3 adventures but I tend not to. Players don't pick up on every clue, especially subtle ones. If they don't know they're dealing with a faction you'll need some other structure to your adventures or they'll seem like a random mish-mash of encounters and locations. Introducing at least one of your factions early lets you focus your game on it rather than have to come up with temporary plots until you're ready to show them one of the main plots. You also have to actually introduce the group or at least let its actions become known to the players or it may as well not exist.
3. Overlap: Your plot threads can interact with themselves directly or they can just compete for the PCs attention. The latter is basically an opportunity cost; often the characters are only able to chase one thread at a time if they want to be effective. The former can involve NPC groups working toward the same goal or opposite goals and everything in-between. This choice is going to help sketch out how events should unfold. If two NPC groups are competing, then if one chalks up a win, the other may well have lost something.
4. Balance: The different threads can be in a delicate balance to start with. This helps emphasize the actions of the PCs and allow them to have an outsized effect on your world. And that helps put the epic in your fantasy. Threads don't all have to be operating on the same scale and indeed that helps space out how they might be resolved. But if you have a thread working against another and their scale is very different, you may need to balance that by having the smaller thread more focused in the area the PCs are operating in. The first example below has something like this: one group operating at the scale of small towns and another across the entire continent. Your threads should also have different goals. Take your PCs as inspiration here. Just because they're all working together doesn't mean they all have the exact same reasons for going adventuring.
5. Helpers: Totally optional, but if you really want to simulate an active world you can let your players have allies and helpers that can work on problems they've chosen not to focus on. Be careful, it should be clear that this is a "B team" or at least the end effect should be less than if the PCs choose to work on a thread themselves. You still want them to be the main characters of your story. But there's nothing wrong with telling them they've bitten off more than they can chew and then giving them a hand dealing with it all.
6. Motion: Plot threads have two different kinds of activity. They can show up in an adventure as a side quest or cameo. Alternatively the PCs may only learn about what happened during an adventure or at the end of it. I think the latter is most common unless your plot threads are interacting a lot with the story you're telling that session. This gives you time to think about it between sessions and reveal information to your players either during the intro to the next session or during it.
7. Replacement: If one or more threads get resolved then you can replace them with new ones. It doesn't hurt to have a vague idea of how this might work to start with but you shouldn't get caught up in it. You don't always know which thread the PCs will choose to resolve first or what sort of scale you'll want to operate on at that point. As an optional side note, if you have the group responsible for a resolved thread make a cameo appearance later on, this is a way of reminding your players that they're having an effect on your world. It may not seem like much but it is a reminder and a kind of reward for playing in your game.
8. Agency: This point is very important! None of these ideas should ever remove agency from your players. If they don't know what's happening or can't affect it, it's just background or setup at best. At worst it may as well not exist. All of the above are tools to offer choices that matter to your players. They don't need to know everything but they should have enough information to make a choice and the options available to actually make one. If they choose not to follow a thread or fail at some point, fail it forward. Let that choice or failure advance your plot in new and interesting ways not bring it to a screeching halt. As GM part of your job is making choices and complications interesting.
Examples:
These are kind of generic because it makes it easier to file off the serial numbers and drop them in wherever you need and adjust the scale. Some campaigns benefit from massive struggles that can rip the continent apart. Others work best at the scale of a single city.
There's a group of bandits and marauders attacking smaller settlements and they take so much their victims struggle afterward. The bandits are actually making off with villagers, feeding a group of Theran slavers who are trying to run a stealthy operation and get the denizens of Barsaive to tear themselves apart using more than one such bandit group. These new backers have riled up the illegal underground scene, causing the shady powers that be to make moves to secure their own base of power.
A Horror is hidden amongst the populace of a small area and it's victims ask the PCs for various sorts of help (but nothing to do with the Horror). Another adept (or group thereof) is aware of the Horror and it's influence but is unable to root it out or deal with the mass of it's victims in an effective way; yet at first they might just sound like an unhinged conspiracy theorist and possibly Horror touched themselves. Militia from one of the local powers are starting to get an inkling of what's going on and are preparing to move in, but not to save the victims; their methods are likely to be effective but quite brutal.
A leader is ruthlessly domineering and controlling but seems somewhat effective at holding off outside dangers. An unorganized but passionate group of rebels is forming to overthrow this leader. But one person or small group within the rebellion seeks to subvert it to their own ends and simply use it as a vehicle to gain power themselves.