A little confused..

[IwantanewPC]

You get graphic quality settings and options both in games and in your Graphics Card's control panel..

Which effect how the game looks? I don't understand.. what if you have anti-aliasing set to x6 in your Graphics card's control panel yet you have it set to off in the options of the game you are playing?

Is it best to just put all the options in the Graphics Card's control panel to the lowest and then change them in the game or what?

 

[Indy500]

The driver control panel overrides ingame AA\AF settings. Unless you set "application controlled".

 

[LoadsaMoney]

Yep, and if games don't have AA/AF options in their settings, then you set them in your Control Panel of your graphics card.