The ceramic "macaronis" have enough open space in them to not interfere with the water flow through the filter, so I think they would be fine. You should have them in a bag so lifting them out to clean the sponge wouldn't be that problematic. A slowish flow rate through the filter helps the bacteria do their job - more water flow, less contact time, less flow, more contact time with the filter media.
I don't use my filter for anything except water flow around the tank and mechanical filtration - I have one sponge which I clean in tap water every week, and that's it! I prefer to keep my bacteria in the tank. Most people don't do this, though.