Well, the standard thing is to have several layers of factions. I'm trying to do something similar in my Eberron game, and one of the first things I did was to sketch out something like a business organization chart. For example, you can decide that your big bad is Vol, and she's been manipulating Sharn for centuries to stage a magical assault on or corruption of Aerenal.
Vol controls the Emerald Claw, but that's too obvious.
There's also that Lich living in the cliffs, who could be a useful henchman.
Who else hate's Aerenal? The dragons. Maybe Vol is finding a way to provoke another war between the
dragons and Aerenal.
Who's good at misinformation and starting wars? House Thuranni, who perhaps has historical reasons to work against Aerenal.
So you've got several layers between the Big Bad and the players when they start out:
Vol-------->Emerald Claw
|
|---------->Lich--------->House Thuranni
|
|---------->The Aurum (high priest of Kol Korran in Sharn)-------->House Cannith (weapons manufacturers)--->
House Tandarak (an assassin's guild)
So the basic plot is that a series of murders is being set up to make it look as Draconic minions are killing
Aerenal citizens, and vice versa. Further (extensive) investigation leads the party to figure out that the assassins are being directed by the lowest levels of the org chart, leading them up to the Aurum. So far it looks like a straightforward plot to stir up conflict in the hopes of selling weapons, and maybe the conflict doesn't yet appear to be between Aerenal and Argonessen, but between Aerenal and some other nation, a war that it sure to draw the attention of the dragons because it is being fought over some Draconic site (such as the caves in Darguun).
As they work their way up to the Aurum, however, they keep getting hints that there are other players--the Thuranni have the job of keeping an eye on the development of Vol's plot, and keeping it on track if need be. Agents in the shadows might interfere with their missions, and just as the party begins to think that they've stopped the assassinations and cooler heads are prevailing....
Wham. Yet another important assassination, this one not perpertrated by House Tarkanan but by a complete unknown. Better yet if it is done is a gruesome and exotic manner. Wham. The Emerald Claw, in disguise, manages to stir up a real military action in the contested country. The PCs have the Aurum under control, they think, but maybe the head of that branch drops a clue in his dying words that his orders were coming from somewhere else...
As war escalates, it's a race against time to find the proofs that the assassinations were arranged, and by whom, and to stop the war before the dragons intervene.
Just an example! Have fun.
Ben