You don't wanna put crushed coral on top of the sand. It's usually pretty sharp and will hurt your rays.
If you can't put the coral in the filter somehow, you could probably get a fry net and put some coral in that near to the outflow of the filter.
But personally, I'd get some serious water changes going. The advice that you don't need to do water changes until the Nitrate hits 40 can be tossed in the garbage can - water changes are for more than just reducing Nitrate. Since you already did 50% and the fish survived it, I'd do another 50% - hopefully that'll add enough Kh to get things stable and work out how to maintain the Kh going forward.