In game options and the cards own driver options are two very different things.
Open up your CCC and use the drop down menu to select 3D. here you have a host of AA/AAA/AF etc options. Note the little tick boxes for enabling AAA, Use custom settings and use application settings. If you go to the All tab you can scroll down them all on the same page.
So you want to un tick the use application settings and tick the use custom settings boxes and enable which ever mix of AA/AF you want to use.
This will work for some games but not others. Its what is referred to as forcing AA through the drivers. There is usually a performance hit for doing this though, again dependant on the game as to how much exactly. cant hurt to try though.