Ideally you want to try to get some of the bio media above the water line. Most pre-filter before the bio media to reduce the chance of clogging the media.
Example of water flow: Water flows out of the tank into a pre-filter (sock or pad of some kind) then flows back up and spills over a baffle onto a drip plate and trickles through bio media. Then the rest of the path flows through submerged bio media, maybe passed a heater or two on it's way to the pump.
Helpful?