When starting a new tank, you must "cycle" your aquarium. This means cultivating the right bacteria in your filter system by allowing nature to take it's course. Cycling is explained in the 7 steps in the picture below. Once your tank is fully cycled, your system will have the right biological and chemical balance for livestock.

You can also start cycle with uncured live rock. Once cycling is complete and live rock is cured, there should be no more die-off or smell from your live rock. Also, waste from your protein skimmer should be greatly reduced. 

Cycling may take 4-8 weeks. Remember, add livestock slowly as livestock creates waste which creates ammonia. You have to allow time for bacteria to catch up and multiply to keep your system balanced.

*Also note: Some people will use small fish or inverts to cycle, but this is unnecessary. Do not use damsels, especially. Damsels are aggressive and you will limit what you can add to your tank later if you do not take the fish out.