Easiest way: Step One: put the fish into a bucket with tank water, media etc...
Step two: take the gravel out.
Step Three: Clean your sand and do an (optional) water change
step four: take a two litre soft drink bottle and cut the bottom off, making sure to leave the lid on.
Step five: put the sand into the bottle till its 1.2 full
Step six: place the bottle into the tank and undo the lid as close to the bottom of the tank as possible. Slowly let the sand siphon out. Repeat till substrate is at the level you need it to be.
This method will reduce the amount of sand cloudiness in the water. Once you have completed step six, you may still need to do up to three or four water changes to reduce the cloudiness and may still need to let the water settle over night it will be ok for you to put your fish back (obviously once you have heated the water up!) once you have the temp up.
Just be aware that you need to be very gentle with the sand, or you will increase the cloudiness!