Do not use bondo on cracks in the gelcoat of the fiberglas hardtops. If the crack is fairly large use a awl to pop any loose gelcoat away from the crack, then wick in some thin Ca glue and hit it with some accelerator(get it at any good hobby shop). This will repair and seal the crack stronger than any other repair substance, even if the glas fibers are damaged, now you can use body filler to HIDE the crack.
If you want to use a bedliner type material for the exterior of the hardtop do not use the rhino, duplicolor, or spraycan crap. The only stuff I would reccomend is the tintable Monstaliner spray and/or roll-on bedliner.