First off.... your cycle is complete. The last thing you want to do is remove the bateria, or too much of it, and cause a mini cycle. Your tank has this beneficial bacteria growing all over everything including the filter media, ornaments, glass, and yes gravel.
One of the best ways to change your media that i have found is to "re-seed" the aquarium. Basically, put the gravel you are taking out, at least some of it, into the compartment or sleeve on your filter that traditionally holds charcoal. If you already have charcoal in there, then there is no point to doing this because it already has this benificial bacteria on it too.
To actually change the gravel its easy. Lower the water to about 20%. This facilitates getting inthere to get the gravel out with out water overflowing. You can leave the fish in there, but remove all the ornaments and driftwood ect. (keep them wet in the 20% take water you took out, preferably in a clean bucket). Use a pourous material to scope out the old substrate. A heavy duty net, or similar material. Once it is all out, you will find your water very dirty. This is normal and from the mulm (fish waste, left over food) in the gravel. do a 50% water change. Clean your new gravel until it rinses clear and put into the tank. Add some kind of dechlor agent and refill with water. Reinstall ornaments drift wood ect.
For the next week, i would keep an eye on cycle threats like ammonia and nitrite. Perform partial water changes as required like you did when you were cycling. Even if you see a small micro-cycle, it will be gone soon.
HTH