Leave it at auto - this will use the best profile for each game based on NV's own testing & optimisations. If you come across a game that doesn't use SLI (rare), you can set the mode manually:
AFR/AFR2 = Alternate Frame Rendering. Each GPU renders frames alternately, giving the best performance boost. Try both modes to see which works best.
SFR - Split Frame Rendering. GPU #1 renders the top half, GPU #2 renders the bottom half. This only accelerates fillrate, so won't give the performance boost AFR does.
SLIAA - SLI Antialiasing. If the game doesn't work with SLI - you can still use this mode. Each GPU renders the same frame - but using a different AA algorithm. The two scenes are then combined giving an AA level twice as high as if SLIAA wasn't enabled. Only a small performance hit for a large increase in image quality.
Some games have an option within the graphics settings (such as COD4) that let you specify if you're running dual GPUs. If that option is present in a game, make sure it is enabled.