first of all are you doin a fishless cycle or a cycle with fish? as soon as the ammonia levels peak you should start doing the water changes in a fishless cycle. in a cycle with fish, the water changes should be started a week after the tank has been set up. ammonia is created from fish waste and excess food. ammonia is then converted into nitrites and then from nitrites to nitrates. you will not remove the bacteria from your tank since it is not only in the gravel, but the water, filter, powerheads and any other equipment also on the decor. if you were to do a large water change, say of about 75% or better you stand the possibility of crashing the tank. you have removed enough of the bacteria that it cannot keep up with the bio load. you can vaccuum your gravel when there is waste present on the gravel. the amount of a water change that you are going to do just vaccuuming the gravel will not crash your tank. probably only about 10 - 20% water change withthe vaccuuming.
you want to keep the ammonia levels at zero once they zero out. since you are not doing water changes that is probably why you still have ammonia in your tank. you can have ammonia and nitrate at the same time. there will always be fresh waste and older waste so to speak. you will waqnt to do a water change as soon as possible to try to remove the ammonia.
when your tank is cycled, the tank will get a bacteria bloom. the water will turn cloudy for a few days. this is usually an indicator that the tank is cycled.
hth
maggie