I just read about this on another site and they suggest small sections and to by some nylons and but the gravel in them and hang it on the side for a week or so just to make sure that the bacteria can transfer in to the sand with out starting a cycle all over again.
http://www.fishinthe.net/html/section-viewarticle-50.html
How do I switch from gravel to sand?
The switch from gravels to various types to sand is a growing topic in the hobby as people are looking for a more natural setting for their fish. This process may take a little time to complete. There are two basic methods to changing your gravel, quick and not so quick. It would be recommended to remove your fish into a quarantine tank for potentially a day if you choose the quick method, otherwise you may want to use the partial change method. This does not mean a fish-in change can not be done, but one must be very careful to avoid damage to the fish.
If you choose the faster of the two methods you will need a very porous bag, such as a pair of new a heavily rinsed nylons or panty hose, to hold a portion of the old gravel for a few days. The process is fairly simple. Start by preparing the new sand by rinsing it thoroughly. Next you need to drain some water into a bucket to reduce your water level a little and give you a holding pen, remove the decorations and plants into the bucket. Carefully scoop out the old gravel into the bag you chose being sure to keep it wet. Please take extreme care if you were unable to remove your fish from the tank while you begin to add in your sand. Continue to add your sand to desired levels and then replace your decor and plants. You will now need to place the bag(s) of gravel back in the tank. Hanging them towards a side will make removing them later easier. If you are wondering why, well that is because your old gravel has established beneficial bio-bugs established on it that you do not want to lose. Placing them in a bag will allow some to transfer back into the tank. The time to complete this transfer will very from tank to tank. You will need to monitor your fish and water until the potential mini-cycle passes. If enough beneficial bio material is transferred there should be no ill effect. The more time consuming method will be safer for the fish that can’t be moved. This method is accomplished by removing only sections of old gravel at a time. As each section is cleared, new cleaned sand is put in it’s place. A good target would be between one third or a quarter of the gravel at intervals of approximately once a week therefore not removing all of the bio-bugs and giving time to recoup any that are lost. The drawback of this method would be not being able to fully remove 100% of the old gravel.