I have a 06 WK and i used the rough country lift also. In the rear it does go on top and it is a lot easier than the front. I put 265/70/17 Nitto terra grapplers on with 1.5 wheel spacers, and I still had minor rubbing where the pinch weld is. Im not positive that you need the wheel spacers but you would probably rub on the control arm bolt like silentj said.
2006 WK 3.7L V6 265/70/17 Nitto Terra Grapplers RC 2" BB lift, 1.5" alloy wheel spacers.
[B][SIZE="4"][COLOR="Red"]RED WK CLUB #17[/COLOR][/SIZE][/B]