I'd split Vigil in a few very different parts. One is dominated by orcs, another one by the Whispering Way, a third by something that's very dangerous for both groups (could be something undead), maybe a fourth which is pretty much empty - and too devastated to be of much interest (for anyone but a resistance group).
Orcs are bullies, and might attract a lot of hate from the players. I'd be careful to show they are bullied and abused themselves, so the players don't get stuck at focusing on orcs. The Whispering Way is a very different kind of threat, subtle, with long-term planning and less infighting. So I'd try to point out the differences between both groups, and allow the party to play each side against the other.
Finally, the adventurers need a reason to not just flee the city. Maybe some powerful undead publicly shows an execution of mortals who tried the same thing. Maybe they find a bit of hope quickly. Maybe they find a mysterious, powerful benefactor who only helps as long as they stay.
EDIT: And I'd be surprised if the forces of Good (mortals and immortals) simply give up on Vigil...
I think the easiest way to provide a reason that they don't just flee the city would be at session zero, where you ask them.
You lay out the foundation: "You're citizens of this city. It's effectively occupied by two forces. Why can't you just leave this place behind you?"
Any player-created reason is going to be a lot more motivating than whatever you can suggest to them.
Even under occupation, there are still rich and poor. Maybe the inner district or whatever is where the lowest of the low congregate. Beggars and thieves and cutthroats trying to survive in this rotting shell of a city quarter. They're safe from their oppressors, essentially being beneath notice, but desperate enough that they turn on each other, if the opportunity arises.
Beyond that, you've got plenty of free-standing adventure hooks in the form of sewer tunnels and abandoned districts, or maybe even a sort of organized crime ring that existed before the occupation and took their operation underground afterwards.
As a player, I wouldn't really know where to start "resisting" offhand. Actual political uprising is pretty complicated. Maybe you could do some research on real-world tactics (especially from time periods that match the setting better), and then have a couple retired adventurer-types suggest some ideas to the party.