I wouldn't put anything under the pumps in the COD (chamber of death). Most of us on here leave that bit empty, as you've seen when you removed the ceramic media it traps all kinds of rubbish and becomes a nitrate factory. Live rock goes into the main display and provides a vast majority of you bio filtration. I would suggest that you get some form of media rack for the carbon, rowaphos etc. These can be made quite easily I believe of purchased from a guy on here.
Hope this helps