Here's an excerpt from an article I'm writing. I thought it might help.
Live Base Rock and Live Sand
Quality Live Rock and Live Sand are the heart of our system. They provide an environment and many of the organisms needed for the food web and nutrient processing pathways to function properly.
The majority of the cool looking life on “premium” live rock like colonial corals, sponges, bivalves, gorgonians, and tube worms will probably not survive in a new tank. The life that is likely to survive and are important to your future reef tank are things like coralline algae, cryptic sponges, bacteria, and small critters. Populations of that life are present in and on less expensive “base” live rock. That is what I would order in this phase.
For this process, the live rock and live sand desired is cultured in the ocean, not a tank. It is provided by reputable suppliers that culture rock in pristine parts of the ocean, harvest it, care for it properly, and ship it directly to you, over-night. The life in ocean cultivated live rock and sand is an important characteristic not available from rock cultivated in a tank. It is held and shipped in water, not in wet paper.
Be careful buying Live rock and sand from a tank at the LFS. Make sure it is truely live rock that was originally cultured in the ocean rather than dry rock that has just bee kept in water to establish some bacteria. This rock may have some life in and on it, but it will may not be as diverse as ocean cultured live rock that is shipped to you direct. It may also suffer from the as many pests as ocean cultured live rock with the added disadvantages of the unwanted Cyanobacteria, Dinoflagellates, and microalgae that tend to come with it.
Due diligence is required when buying live rock and sand. Researching and talking to suppliers is absolutely necessary. This is the most expensive and most important purchase you’ll make. Don’t skimp, but make sure you get your money’s worth. Shop around. Some suppliers provide lighter rock than others. All other things being equal, “Lightness” is a valuable characteristic. Not only does it indicate more desirable porosity, but it means you will receive a greater volume for your money. Some suppliers will also negotiate prices if you contact them directly.
Live Rock Expectations
Today’s manmade live rock is much denser than the more porous rock we got back in the good ole days. If you were around back then, lower your expectations for the volume of rock you will receive. Order about 1 lb. per gallon of “Base” live rock and 1 lb. of live sand per gallon. More rock, up to two a total of pounds per gallon, is good. Make sure all is shipped water. Remember, this it is the life blood of your future system. It will replace all the expensive equipment we might otherwise have to buy to reduce nutrients and to prevent or combat the problems that would be encountered if trying to establish a reef tank without the live rock. I firmly believe that every dollar spent on live rock & live sand saves two or more during the life of the tank.
Let’s talk about the bacteria
We hear a lot about the nitrifying and denitrifying bacteria that are responsible for the nitrogen cycle and the process for establishing them in a new reef tank. You’ll see lots of discussion about “Cycling a tank”. We will not need to worry about this process. What is important to emphasize here, is that the live rock will contain more than a sufficient quantity of these bacteria to manage the ammonia produced as we add life to the system as instructed. No additional bacteria or ammonia additives are necessary for the growth of this bacteria. This type of bacteria is called autotrophic bacteria. In simplistic terms, it can derive food from CO2 and the ammonia, nitrite, and nitrate we are trying to get rid of. This is important… DO NOT ADD AMMONIA before of after the rock is added. There is no need to “Cycle” the tank prior to adding the rock.
There is another type of beneficial bacteria at work in our system. These are heterotrophic bacteria. These bacteria can’t derive their carbon from CO2 and must uptake organic carbon instead. These bacteria are also present in great numbers in the live rock and sand. They are partly responsible for the process that yields the dissolved and particulate organic compounds that drive many of the nutrient processing pathways and provides a thread in the food web in our systems.
Bacteria exist everywhere… yes, even the ones that colonize the rocks in the ocean. They will colonize anywhere when the conditions are right for them to grow. Some of these bacteria are beneficial. Some are destructive. They compete for the same chemical and organic compounds.
Once a particular strain of bacteria is established, it is harder for other strains of bacteria that have similar requirements to compete. LET ME REPEAT THAT… Once a particular strain of bacteria is established, it is harder for other strains of bacteria that have similar requirements to compete.
We are trying use this to our advantage. We’ll establish the bacteria we want by starting the system with live rock and sand containing large numbers of the autotrophs and heterotrophs that we want. That makes it hard for other strains we don’t want to compete and get established. Given proper care and attention, other less desirable bacteria won’t be able to compete or cause problems.
So why can’t we just seed sterile substrates like dry rock with live rock and sand? This is a popular idea that just doesn’t work as well as theorized. The bacteria present in the live rock used for seeding can’t propagate fast enough to outcompete the bacteria already present. In addition, the surfaces that are not live rock may not provide a suitable habitat for the bacteria. Nature will supply other bacteria that can survive on the bare surfaces long before the more desirable bacteria can get a foothold. That will allow for the ugly stage that we are trying to avoid.
Discouraging pest algae… The live rock and sand, along with the organisms they contain, and the biofilms that cover their surfaces, are a deterrent to pest algae also. These organisms: 1) Reduce or bind nutrients needed for algae to grow; 2) Compete for substrate on which to algae might otherwise grow; and 3) Consume the algae as it attempts to get a foothold.
You may ask what all the above gibberish means. Well… It means that starting our system with OCEAN CULTURED live rock and live sand greatly reduces the risk of prolonged periods of microalgae, Cyanobacteria and/or Dinoflagellates infestations that are commonly referred to as “THE UGLIES”. It also means we will not waste time and money battling these unwanted pests.
Prepare Live Rock and Live Sand
There is little to do to prepare these items if you ordered from a reputable supplier that ships the items in water. It is important that you make plans so you can do the preparation immediately upon receipt. Each supplier will provide instructions for preparing and acclimating the new items. Follow their instructions carefully and start the task a soon as you possibly can. I do try to pick macroalgae and plant life off of the rock. They will become pests if they don’t die off. In case the instruction do not include it, preparation should always include a bath in high salinity (1.043-44 ppt) saltwater. This causes the many of the critters hiding inside the rock to emerge. The pests can then be removed and good hitchhikers can be added to the tank. Tweezers and gloves are a good idea for this step. Swishing the rock around in the high salinity water helps also.
Aquascape the display tank with prepared live rock
The prepared live rock is the first strategic addition of life. It harbors organisms that are net nutrient users and also provides a source to populate the system with nitrifying and denitrifying bacteria.
Stop all pumps. Stack & secure the Live Rock in the display tank to aquascape to your liking. Secure it with two-part epoxy putty as you build your reef. Don’t get crazy though. Remember, this is base rock that is intended as a landing spot for future corals.
Do not mix in dry rock to enhance the aquascape. It will just provide sterile substrate that might provide a foothold for undesirable organisms.
Turn on the display tank lights. There is no need to start with high intensity lighting right now. If possible, set intensity level just high enough to encourage Coralline Algae growth in the display tank. Run the lights for about 8 hours per day for now. If possible, run only the blue portion of the lights and set the lights to ramp up and down over the time period selected. These steps will discourage microalgae growth while the tank stabilizes.
Check the live rock and sand for pests
Take some time to check out the live rock. While undesirable hitchhikers should not be a big problem, removing any you can find now is better than waiting until they reproduce and become a problem. Look at the rock at night with a red light. Identify the critters you see moving around. Remove the ones that might be harmful. There is a lot of good information on the internet to help you identify these critters, determine if they are undesirable, and how to trap, kill, or otherwise remove them. Do not use any potions or chemicals to rid the tank of creatures you find. If you can’t remove or trap them, we’ll add critters to deal with them later.
Add some hearty, nonaggressive fish
Cardinals and Dartfish are good candidates for this addition. Unless you intend to have an aggressive tank, avoid Damsels and Clownfish for now. I know, Clownfish are very desirable. You need to wait though. They are just too aggressive and territorial to be the first fish in the tank. Please note that we are not “Cycling” the tank with these fish. Ammonia will not rise when they are introduced.
So, why is ammonia not a problem at this stage?
The live rock in the system has more than enough nitrifying and denitrifying bacteria to support a fair number of nutrient producers (fish and invertebrates), but let’s keep it reasonable. One small fish per 25 gallons is about right. The goal here is to provide some ammonia input to start nutrient processing pathways. We don’t want make the ammonia input too high. That will result in excess nutrients that might encourage undesirable organisms to get a foothold.
Feed lightly and only once per day for a week or so. While I wouldn’t expect you to count them, target about 5 or 6 Mysis or Brine Shrimp for each fish per day. This provides a controlled input of ammonia to feed organisms in the live rock and spur more bacterial growth. Increase feeding after about a week. Avoid flake and pellet food for now to limit phosphate levels.
