It's generally preferable to enable AF and AA with the game, but many older games don't offer this option, so you're left to force them via the drivers. nV has per-app settings, though, so it should be relatively simple to enable AA and AF either via the game or the drivers, depending on the game.
But the 6800 should be powerful enough to just enable 4xAA and 16xAF for everything at 1024x768. At 1280x960/1024 in newer games, you're probably going to want to dial down AA, as you'll be bumping into bandwidth and memory size limitations.