Intrigue and political navigation can be hard to run. There are a lot of moving pieces, and it is a game more about subtlety and reading people than it is about killing and fighting. Most systems aren't built to handle intrigue, and even games that purport to have 'social interaction' as one of their pillars of play don't actually provide mechanics or much in the way of suggestions for playing this out.
For my own uses, when needing to prepare multiple NPCs for an intrigue attempt, I've found there are three things that can be good to have on hand - in addition to whatever normal stuff I prepare to be able to play the character. This does make an intrigue NPC more work, but you knew that by default when you chose to make a path of adventure for intrigue. Consider it this way though, you're choosing social mechanics and spygames over combat. So really this is just your combat prep time put to a different use.
Fact 1: An Embarrassing Secret
Everyone has secrets, and in an intrigue plot everyone is going to have multiple secrets. The Embarrassing Secret is the entry level secret. It is something that the NPC in question does not want getting out. Not because it will destroy them, but because it is embarrassing in some way. This could be as small as the fact they have sexual proclivities they'd rather not get out because it destroys their image as being a staunch traditionalist on family values, or it could be that they have a family member that commits crimes that they are keeping out of the paper to avoid assosciation.
The Embarrassing Secret is something that can be used for leverage on an NPC but it doesn't necessarily control them. It is good to know, and a player can help to hide it - or resolve it - to get in good graces, or they can exploit it to be taken seriously. Just remember, it is leverage not a Rod of Control.
Fact 2: A Devastating Secret
This is the secret that is more of a Rod of Control. The Devastating Secret is just that, a secret that would be devastating to the NPC if it got out. It could lead to their death, loss of position, or otherwise just take them out of the game. The point is the NPC will do a lot to keep this secret from getting out, and a PC can get a lot of leverage over an NPC by knowing it whether they use it to blackmail the NPC or protect it for the NPC is up to them.
Just remember, this is the type of secret that the NPC would prefer no one had. Just knowing this secret exists can make the PCs dangerous to the NPC. So even if the PCs are using it to control or help the NPC, the NPC may still want out from under it.
Fact 3: What Hold, If Any, Someone Has Over Them
Finally we need to know what hold, if any, other characters have over them. Essentially, if the NPC is working or being coerced to work with another NPC, why are they doing it and what do they get out of it? Are they having their family held as leverage? Does someone else know one of their secrets? Are they being paid under the table exorbitant sums? Is someone feeding their addiction for rare underdark drugs or exotic, fluffy creatures to hug and snuggle when they're sad?
Between The Three
Between these three facts, along with my normal thing of defining the NPCs goal and their desire, you have a good picture of how they can work in your intrigue plot. You give them vulnerabilities to defend, levers for other characters to use, and things they are working towards.
Then all your PCs have to do is throw a bunch of monkey wrenches into the mix and you have an intrigue based plot.