your primary filtration is from bacteria living in the substrate and live rock, which are regularly cleaned of detritus if you have a decent clean up crew of worms, snails, etc. When your tank cycled, it built a multi-tiered population of bacteria that process ammonia, nitrite and nitrate. The same bacteria are probably living in your bio-balls by now - which is exactly what they're for. However, since the bioballs never get cleaned like the sand and rock in your tank, the detritus builds to a point where the resulting nitrates are more than the system can easily handle, and you'll likely end up with climbing nitrate levels down the road. That was my experience, and apparently that of many others. What I did was to gradually remove the balls over about a month's time to allow the bacteria populations elsewhere to pick up the slack. As far as replacement, you can turn that section of your sump into a small refugium with a bit of sand and rock of its own, and allow detrivores to live in there as well. It will extend your filtration capacity, and possibly dampen some of the splash noise. You'll need to do some baffling to prevent the sand, etc. getting sucked into your main pump and/or skimmer. hth
Any other questions, feel free to ask 
