if your top sticks up too high on one side ,either the top was installed incorrectly or the mechanism is out of adjustment. does it raise and lower evenly or does it want to twist? this might be enough of a difference to keep the boot from fitting correctly.
the idea is to slide the boot into the channel on the rear of the seat. next you fold it over the seat and when the top is down, over the stack ( the lowered top assembly). then attach it around the perimeter with the plastic clips and snaps on the interior panels. in order to raise the top, you would unfasten the clips and fold the boot over the rear seat. when the top is up, fold the boot over the seat and lay it on the well liner while still attached to the seat.
having said that, i wouldn't suggest doing it that way unless you are absolutely sure everything is dry. any moisture in the well liner or under the boot will cause mold or mildew. at the least, an unpleasant odor.