It depends what you are better at using. I am lucky, I know how to lay up glass. (Used to repair fibreglass boats). If you have never used glass before I would suggest bondo, unless you have alot of time to experiment.
Bondo usually cracks because either too much hardener has been used or there is not enough support for it. It isn't suppose to be all that flexible, so if the panel that you are putting bondo over flexes then of course it will crack.