You might be missing some parts.
There should be a styrofoam platfoam for the tire to sit on at the bottom of the well. The tire sits upside down with the lug side facing down.
Now there should be a plastic bucket that holds the scissor jack and handle in place. You have to spread the jack out to fit the bucket.
Now the jack (which is inside the plastic bucket) fits down inside the wheel.
Now there should be a plasic clamp that threads down on the stud to hold the jack in place. Since the jack is inside the bucket, which is inside the wheel, everything gets held very snuggly.
Now your ply-board cover goes over the wheel well.
Now a large plastic (frisby style) nut goes over the ply-board to hold it down.
Did you get all that?