I hate to tell you this, but you need put your rocks on the sand. The sand will slowly dissolve over time (this is good, helps keep your water stable) and will critters digging around them, the sand can shift causing a rock slide. Which, im sure you realized is devastating in any tank.
*need to put your rocks on the glass, she means. If they are sitting on the sand, it is easy for them to topple over. They need to be on a sturdy, stable base.
If you add dry base rock it shouldn't kick of a cycle because there wouldn't be any die off.
Personally, i would take it out, or put some rubble in there to increase your filtration. and then maybe once a month run a filter for 3 or 4 days to "polish" your water.
In marine tanks, the filtration is done by the bacteria living in the rocks and sand, not filters. Those are a freshwater idea that doesnt translate very well to marine tanks.
Some particles will get trapped in there, but not like if you have filter media in there. If you can, why dont you put cheato in the filter box, making that a mini refuge.
Also, this is saltwater, the rules are different, dont worry about freshwater rules on a saltwater tank.
I swear cheato grows in the dark, but for lighting just use one of those squiggly blubs. Works great. You just have to change the bulbs every 3 months, because after that time the light intensity that they put out is pretty reduced, even if you can see the difference.