with the top down look in the well where the top sits. you'll see behind where the rollbars are that there are lil chrome colored snaps. it's what the stock tonneau covers snaps into.
another thing that i find does make the top sit lower is, when the top is up and your sitting in the car look above you, theres a bar. when putting the top down, push this bar towards the back of the car as the top goes down. if this bar isn't pushed back the top won't sit at it's lowest and you will not see the snaps i'm talking about.