Siphon as much off the rocks as you can...I use a 1/2" hose for this since it lets me get into the cracks of the rocks and also creates a nice strong, focused suction with the smaller hose. This also allows me to siphon the sand by just pulling the top layer of cyano with some sand attached.
If you really need to keep the sand, you can always put it into a cup or small container and rinse it in a water/peroxide mix. This will kill the cyano on the sand...but also any beneficial bacteria as well. But, then you can add it back to the tank after rinsing it and letting it dry out...just sprinkle it all over the tank rather than dumping it into one spot. I was doing this for quite awhile to save my sand and it seemed to work. But, I was only taking out maybe a cup of sand at the most. I wouldn't probably do this if siphoning large quantities of sand out.
Then for maintenance, daily squirt the rocks with a turkey baster to break up the small newly forming cyano bits so they are put into the water column and collected in your filter sock.