Use a fine mechanical/polishing media (On top) water immediately after the course mechanical media (bottom). There is no reason to do it later. The biomedia should be dealing with the cleanest water possible to be the most effective and preventing getting clogged or smothered. The biomedia should be the last stage. If you use carbon, peat, crushed coral, etc that should go after (Middle) the mechanical but before the biological. The mechanical should always be the first stage (course before fine obviously).