You should always use the the in game options to fiddle with settings if possible. I'm assuming you've downloaded the nTune control panel. It's forceware, so whatever setting you choose in there will be the setting that will take effect. The only reason you should use the nTune is to try and use a feature that is not available normally. Always have it set to let the program decide unless you need something specific. A good example would be for oblivion; It will only let you set some of the settings in game, i think it will only do X2 AA or something. I used it to increase beyond that setting, to 8x. Just because you can force it, doesn't mean its always going to work. Some games are simply not meant to run with it, and will look worse.
Thats a fairly beefy video card, and if you have a setup to match it your going to have no trouble running games at max fps. If you try and run older less demanding games, this might actually hinder you. For instance, playing Doom III on my computer, it can render nearly 250 frames per second. Most people would think that is a good thing, however it is not. Most monitors can only display 60 frames per second. You can check your monitors frequency to see how many frames you can display. A DVI connection is limited by 60, and most LCD's are also. Some CRTs can display up to 75. You can check your default setting in windows, it will say 60hertz most likely. (Not to be confused with response time, that can cause ghosting). Regardless your monitor will not be able to display the massive amounts of frames the card is sending it, so you will end up with a 'tearing' effect, where you see half of the next frame ahead of time. This is where you will likely need to use your nTune control panel to force a mode called Vsync, or vertical sync. It will keep your FPS @ 60 or lower, preventing tearing.
Other then the odd setting, you should not need to use your nTune settings.
