For normal daily use, you should have a soft liner in the roof well. A lot of people have bought the "Muz mat" for this purpose. I just velcro a piece of fleece in the well. Also, I have installed a static cling tint to the outside of the plastic window to protect it from scratches. Some people use a "roll" to minimize the crease. This should also be good enough for when the hardtop is on for months at a time. If you have an '02 with a glass window, none of this matters.

 

Here is a great pic of the roof latch and the hardware.
Mind you my bar is under construction so when the plastic interior panel is put back on you would not see any of the mounting bracket.

 

Thanks for showing the actual underside of the hardtop. I understand that the underside of the Miata hardtop is just painted metal. This looks much better. Thanks again. My hardtop should be delivered any day. As I live in the Chicago area, it will be a welcome addition for the winter.