To start off with, I siphoned sometank water into a big clean container. Then I caught all the fish and put them in there. I then used my hands, a cup, whatever to take all the gravel out. Make sure you put it in a watertight container so you can keep some wet. You'll need to use a bit of the gravel in a piece of pantyhose to lay on your sand to help keep it from cycling. As for the sand, I used an old 1-gal plastic pitcher, filled it about 1/3 up with sand, and rinsed it at my sink. I'd fill it up with water, then move the sand around with my hand (slowly or it'll make a big mess!) for a few minutes, let it set a minute and poor the water off. I'd do this 6-8 times per pitcher of sand. Then I'd take it and slowly pour it into the tank. (You should still have about half your water in the tank.) Just keep doing that until you have enough. Then you can add more water, plants and fish. Just don't forget to use dechlorinator when you add the water.
It never has messed with my stats, so I don't see why it would change yours. Remember, add that stocking of old gravel as soon as you get the sand in place so it can start transferring the bacteria. Also, it will be cloudy for a little while, but it will clear up. If the fish act like they aren't breathing too good, you can add an airstone. And make sure to keep your sand turned, too.