re: Just got back into saltwater aquariums. got sick deal

Miracle Mud or live sand is used in the refugium to create an anaerobic environment for denitrifying bacteria to thrive. In order to create that type of environment, you need a good 6-8 inches of substrate.

As for what type of algae to grow and further reduce the nitrates in your system, I have always found Chaeto to be more readily abundant and easy to maintain. It grows in a ball, and so every once in a while, just tear the ball in half and throw one half back in and the other in the trash.

As for seeding the rock, deacon is right- it will eventually become seeded over time if you add some live sand or live rock to your system.

If the live rock needs to be cured, now would be a good time to throw it in with the old rock, put a heater in there, cover it and let it cure for the next 4-5 weeks. Or if you get rock that has already been cured, just set the tank up like normal and add both the "dead" rock and "live" rock together and let it cycle for a few weeks.

Also, those bioballs in the sump are widely considered to be nitrate factories, so I would suggest dumping them.