*D&D calls Spheres of Influence of the gods, "Spheres" or "Domains" depending on the source material. So the things that the particular god has power over*
I just wanted to share an experience with running a similar campaign. In my campaign the good gods had basically destroyed the concept of chaos, so everything would remain largely the same for ever. Far from perfect, but not too bad, utterly unchanging. If the world was to ever change, chaos has to be unleashed. This is something that the dark gods were working towards, as was Avandra. The PCs wanted to unleash the chaos, then defeat their enemy gods once and for all.
This ended up being largely unsatisfying. The thing is, every time the PCs won a victory, they were left wondering if they had done the right thing. Too many victories were won at a large cost, having done unsavory things. In the end, there was never any real cause to celebrate. As much as we might like to play around with other ideas, D&D is really best when the PCs are securing heroic victories and saving the day. When you are considering a grey campaign, I think you need to consider how the players are going to feel if they reach their goals.
To contribute: I played in a game where the battles of the gods were raging across the world. The GM I think expected me to join the 'good' gods. Instead, I chose to throw my lot in with mortality. I ended up working to remove all of magic from the world. I figured that humanity would survive much better if there was no such thing as Dark Lords, Necromancers, Sorcerer Kings or Deities. It turned into a great campaign, I basically ended up with the Eternal Sovereign ED and in my land, no magic or divinity functioned at all, not even my own. The point of sharing this was that even in a grey campaign, it is important to have a 'puppy', something that the players are working to protect and care for. Simple selfishness or complex machinations that border dip into the immoral are not generally satisfying in the end.
So if you wanted a similar theme, you could play up the carnage that happens in the mortal realms when the gods fight. The PCs could find themselves as champions of the mortals, just trying to protect them from the excesses of both the good and bad gods. Like Wrath of the Titans I guess. One other cool thing is that this allows for some very diverse characters. For instance I was an atheist paladin who ended up channeling off the hope of the common people, there was a regret filled Bane Blackguard who vowed to kill his own god for what he had done in his name (Bane approved of his moxie and did not strip him of his powers, instead saying "give it your best shot"), we also had a Drow Priestess of Lolth who came to understand that her people were only hurt by their goddess, she just wanted the fey to reject all deities and reunite (when Lolth found out and disowned her, she channeled off the archfey who thoroughly approved of her plan).
