I've been reading about Plenum filtration that allows anaerobic bacteria to be established deeper in the substrate. Would I essentially accomplish this by just turning off the undergravel filter in my established aquarium? Would this reduce nitrate levels.
Do you have any fish in your tank, or any inverts?
If it were my tank, I would:
Drain 5 to 10 gallons worth of water and put them into two buckets, and put your livestock in them. Drain as much water as possible and put them into other buckets, and put your rock into those. You should now have a tank with 'disturbed' substrate and polluted water.
Remove the crushed coral subtstrate.
Remove the undergravel filter.
Clean up what you can, then place your wet rocks back into place, then fill on all sides of rock with 1" to 2" of aragonite DRY sand, that's been rinsed thoroughly beforehand.
Put in 5 to 10 gallons of newly made saltwater, pour in slowly. Then fill the rest of the space with old water and livestock. Turn on everything, sit back and wait.
It's a pain, but it's better for the tank in the long run. Just don't remove the rocks or disturb the sand UNTIL the animals are out of the tank, and when most of the water is out of the tank. This way you don't waste what water you have, and don't pollute your rock with any gas or ammonia being released from the old substrate and filter.
Like I stated in another thread, there's nothing in a saltwater tank that really takes up excess nitrates, unless you have a refugium. All an undergravel filter will do is pull in waste and give it a place to rot. Since there are typically no plants, this excess nitrate needs to be pulled out through water changes each week.