There's no reason why you couldn't put it over the sand. The only thing I'd worry about is your fish digging into it and disrupting pockets of poisonous gasses in the sand if you're not stirring the sand anymore.
Is there a reason that you want to put crushed coral in as a substrate? I'd imagine it would get covered with algae after time. If you want to use it to buffer the water but aren't set on using it as a substrate you can put it in an old nylon and into your filter.