Here's the deal ...
You can EITHER run your cards in SLI (in which PhysX processing, if needed, will 'share' resources with the rendering duties on one of your two cards), OR you can dedicate one card to the regular rendering, and one to PhysX, thus 'breaking' your SLI set.
The ONLY TIME you MIGHT want to 'break' your SLI and dedicate one card to physX is if a game comes out that's generally pretty easy to run, graphically, BUT the PhysX component is VERY taxing.
The only games I can think of offhand at this moment where you *might* want to do that are: Alice: Madness Returns, Mafia 2, and maybe the Batman Arkham Asylum.
For general everyday usage, tell NVCP to run PhysX on card 2, but DON'T dedicate it to PhysX (because that 'breaks' SLI).
Very, very occasionally you might play a game, like I say, where it might run a little better if you change to the other configuration, but it will only ever be a game that supports Hardware-Based (GPU) PhysX. And not even all of those ...
Edited by brettjv - 2/15/12 at 4:10pm