You set the spare tire into the space under the hood, with the face of the wheel at the rear and the open space inside the wheel accessible from the front.
The spare tire bolt has the flat plate attached to it.
You reach through the front of the spare tire, and the bolt goes through the big center hole of the wheel, into the hole in the vertical support behind it. As you screw the bolt in, the flat plate is bigger than the center hole of the wheel, and will come into contact with the inside face of the wheel surrounding that center hole. Keep screwing to firmly attach the bolt - this should "snug up" the wheel so that it is in contact with all of the rubber bumpers that you just replaced on your car.