Java fern propogates itself through rhizomes, so you want to plant it below the gravel. When you gravel clean your tank, just go carefully around the plants. Clean next to them, but regulate the suction power of your gravel cleaner by squeezing the hose as you clean so that the plants are not too badly disturbed.

You can slightly cover the rhizome (large dark brown "root") but it is recommended not to. Usually people will attach it to driftwood or a rock using fishing line until it attaches itself. If you want it on the substrate you can weigh it down or keep it in place with a rock until it attaches to enough gravel to stay put. I usually hoover around plants only and don't plunge right in. Once every 4-6 months I uproot the plant and give the gravel a good vacuum. Then re-root. In densely planted tanks I just hoover and re-root every 4-6 months 1/2 or 1/3 of the tank with a weekly water change until its done.