We put the cover on after it was open a couple of times, and then figured out that it's easier to put the cover on first, and then open it up
. No ladder needed.
We pad each of the lower four corners at each bed (upper shells) (we don't have an SL), and wrap the hold-down clamps at the bottom of the swing arms. I also put some padding around the license plate in the back. Also pad the lower four corners of the bottom TM shell and the ends of the bumper (ours is square).
Another thing I do is to roll up the flap where the door goes onto a pvc pipe (3/4" I believe) (I tape it with duct tape to get it started). I've found that it's much easier to keep it up out of the way of the door with that pipe in there.