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Let me first say this is a great idea and very doable. I myself ran Racing to Ruin with each of the players working (secretly) for different factions and gave them different faction missions to accomplish (secretly) along the way. It worked great and most of the players didn't know WHO the other players were working for until much later when many laughs were had.
Anyway, the important thing to remember is that PvP can be VERY dicey. It's a fine line to walk. 20+ years of GMing experience, I've seen players' feelings hurt too many times due to PvP. No matter how much they say they're cool with it before they get into a fight with another PC, by the time the fight is over, someone is ticked off. And let's face it: no one likes "thier" side to lose. The important thing is to make sure each side feels like they're winning something if they succeed.
I'll give you the tale of my group as an example.
Spoilers for obvious spoilers.
As I said, they all started "openly" working for the Government faction. One PC wanted to join the Pathfinders, so he was leaving trail markers for them. One PC was an ex-pirate so was leaving markers for Kassata and her crew. Another was good friends with Sasha, so agreed to help the Red Mantis so they'd get off her back. The last PC was a greedy SOB and wanted to help the Consortium so carried a scrying ring for Dargan.
So they end up "winning" the race and (barely) getting the Government faction to the city first. Then they set up camp with the Government and realize what a bunch of racist so-and-so's they are and leave. They set up a join Pirate/Pathfinder camp using the faction prestige they'd built up secretly with those two organizations.
Of course I still had one player secretly working for the Mantis and one for the Consortium.
The Consortium player was assigned to secretly assassinate the Pathfinder camp's leader. He planned this out over several weeks and we finally had a one-on-one session after the game as he successfully killed Amivour Glaur. This left my Pathfinder PC as the senior guy in the valley so he took over the camp. Worked well.
After the Ivo Haigan events in Book 4, the Aspis camp was left without a leader. My Consortium player had enough prestige that he was the next most senior member and took over the camp. This meant I had two competing camps and it looked like the Pathfinders were going to be the clear winners in the race to claim the city. To ease this loss somewhat for the Consortium player, I added a gold vein inside the Flooded Vault. He was ok with losing the race to the Pathfinders when he knew he was dropping his camp ontop of a (literal) gold mine and could rake in some profit for the Consortium.
The Red Mantis player also eventually moved out of the Pirate/Pathfinder camp and joined the Mantis/troglodyte camp. I assigned him kill missions against the various NPCs in the valley and vaults and their primary goal was finding the lost mantis blade. He found this for his faction (hidden right under their noses) so felt like his faction had "won" as well (even though they had come no where NEAR winning the race for discovery points and claiming the city).
So you see, you could easily have two groups of PCs working from 2 different camps to claim the city. In my case, the party just met up each morning to go exploring, but they were really working to clear the districts of the city for their own faction's explorers to be sent in to gather discovery points.
The vaults will be a little tougher though. You'll either have to have the focussing gems for the portal magically reappear after being taken (kind of lame) or the parties are going to have to work together to open the portal to Ilmurea below. Or you might be down to one table of players by then anyway. :)
Again, for my game, I assigned the PCs faction missions that struck against the other PCs factions, but never against the other PCs directly. When they approached me with the idea of working for different factions I told them straight up that they could accomplish their missions without any direct PvP... and they did.
Those are just some of my rambling thoughts on the matter.
Cheers!
Jenner wins. He said everything I would, but he has experience to back it up!