Gixxer, I think we are not talking about the same things.
You have a S AWD model, do you have the roof side rails? I don't know because in Canada the S AWD Rogue have them (not the S FWDs), but I think it is different in the US.

From what I understood, the OP has the roof side rails but not the cross rails, and the holes he is talking about are the holes which are used to connect the cross rails to the side rails, not the ones attaching the side rails to the car.

But I may be mistaken, needs more information/clarifications.