I have always used bleach unscented 1 gal to 300 gal of saltwater and let it run for 24 to 48 hrs. It will kill everything and clean all your rocks and pipes equipment etc it passes through.
Once it's done it's job I drain all the system and let it sit dry for atleast 48 hr, and longer if you have deep sandbed.. once dry fill water back up in tank, I usually let Rodi unit fill tank up as it's all dead anyways then mix salt in it and run carbon or poly filter for few days.
Cycle the tank it's brand new all over again.