How much sand do you have in the tank now?
How long has the tank been set up?
Are the rocks on the bottom of the tank now and you don't want to burry them under 4-6 inches.
Describe your system, size, filtration.
How much sand do you want to add?
Pulling your rocks out of the sand might uncover some buildup that may pollute your tank some, anyones guess as to how bad. If you have good filtration and run some fresh carbon while your doing it and have a water change ready just in case you have a bad spike of ammonia.
you might want to get either some base rock or some more liverock and either leave your liverock alone and build your sandbed around it or place some baserock down under the liverock.
Most people will, when starting a reef tank put a 1/2 inch or an inch of sand down and place the rock on top of that then build the DSB. You will not want it on top of a DSB as any sand sifting, moving fish or the like could cause a reefalanche and that would not be a good thing.
I personally put a layer of eggcrate down, layered sand on top of that, placed my baserock on top of that then added the rest of my sand for about a 2" sand bed. I prefer shallow sand beds.
The choice will be yours here on either placing baserock under your liverock or using more liverock, or no more at all, but either way you will loose some liverock under all that sand. There are ways around it though. Some people have built pvc stands for the liverock. If you feel like doing that someone can give you directions, or even pvc feet siliconed to the liverock, either will raise the liverock and you will loose less that way.
Any container will be fine for your livestock and they can stay in there for a long time, as long as you maintain the water chemistry, temp, and all.
Let me know what your goal is as far as depth. I believe most reefers would agree that you should not place your rock on top of a DSB.
Thomas