The gravel in the tank is one place that the beneficial bacteria live. These bacteria help to break down waste products from the fish. Actually, some people (myself included) will grab a few handfuls of gravel from an already-established tank to add to a new tank to help with cycling.
I would avoid drastic cleanouts of water, gravel, and filter media all at once. I like the filters that have 2 cartridges in them; I change one at a time. Those good bacteria, without them, a tank is doomed usually.
