This is my recomended sequence from doing this last year.

* I worked the dents out the best I could and polished the trim. I couldn't get all the dents out on mine.
* put some tape down on the paint but not to far in as it will be difficult to get out. If you can get a second person to help you will be safer to keep from scratching the paint.
* Space out the clips inside the molding and test fit. The clips only help to keep the molding from pulling up.
*The bottom side of the molding will have holes for self tapping screws. This is what keeps the molding in place.
* I used the stype claulk to keep water out but is not needed.
*While test fitting make sure the ends of the molding fit with the 1/4 glass felt strips.

There is nothing here that is very difficult. Just keep the molding tight to the body when installing the screws.