AFCAD files should be placed in:
Flight Simulator 9Addon Sceneryscenery

But AFCAD files will rarely change the look of your scenery. Instead, it simply shuffles things around. For example, if you install new scenery and in the new scenery, the runway has moved from its original position, AFCAD will be used to tell Flight Simulator the new position of the runway. It can also be used to add additional parking and gates.