Skipper, When you take off your wheels and then remove the bearings and hubs, the backside of the hub(opposite where the studs stick out) is what gets turned. The rotor attaches on the back side and it need to run true to the hub.
I did have to use a 1/8 inch spacer between the spindle and hub to make clearance for the brake pads. (Some of the kits have an offset made into the caliper bracket).