I just did what you are asking about and I had no problems with a sandstorm when I took out the coral and put in the sand. After getting great advice from people on here, I decided to do it one quarter of my tank at a time. Now my tank is only 40 gallons so each section was fairly small. I only had three fish in the tank when I did it but they were fine during the ordeal. First I took a new dishpan and filled it 2/3rds of the way full with pool filter sand. I went outside and rinsed and rinsed the heck out of the sand in the dishpan. I drained the water the best I could since I had used tap water and let it sit to dry out somewhat. The next day I used a plastic cup and scooped out the coral from the back corner of the tank. I did have to do some rearranging of my live rock since I knew I would be moving it around for the next few weeks. I tried to put the main pieces on the bottom in each section as I did the change in that area so I could put the rock on the bottom of the tank and put in the sand around it. Anyhow, after scooping out the crushed coral I then used another plastic cup and took a scoop of the cleaned and still damp sand. I gently lowered the cup into the water over the area I was filling so that any sand that spilled out of the cup went where I wanted it and not on the rock. When the water fills the cup of sand, you will get a little spillage but not much if you do it slowly enough.
By doing it this way, I had virtually no cloudiness to my water while the sand settled. I simply took the cup down to the bottom and dumped it out and went for a refill.
I had read the other ideas of using a baggie or a piece of pipe but the cup was super easy and also I think would be easier to refill than the baggie idea. It just takes a little longer I'm sure since I used a 12 oz cup. The tube idea on here is a great one too, I was just too lazy to go and get a piece of plastic tubing!
Regardless of my good intentions, I got carried away on week 2 and ended up doing almost the entire left side of my tank. I was afraid I would get a mini cycle but my levels stayed at 0 and I never had a problem. So I ended up doing the changeover in 3 weeks instead of 4. As recommended on here though, you should probably stick to only a quarter of the tank at a time so you don't end up with a mini-cycle.