Cleaning does not mean that you will need to do thorough scrubbing for complete removal of scum trapped in the compartment because those are usually colony of beneficial bacteria growing in it. In fact, the correct method usually involves a gentle rinsing which is more than sufficient to keep the bio balls in tip-top condition. In fact, another technique, which I normally employ, is by removing only half the bio balls quantity for the cleaning and leave the rest untouched. This will ensure that there is still presence of beneficial bacteria, which could regenerate and repopulate back itself again. If proper maintained, these bio balls will continue to serve your aquarium needs for many years and still remain fully functional.
Bio balls are mostly used in freshwater aquarium system rather than the saltwater tank setup. Main reason is because saltwater biological load is usually more demanding and the needs for better system means that the use of marine live rocks is more effective for water treatment purpose. However, this does not mean that you will need to completely remove the bio-balls because if you already have it running in your aquarium system, combining with marine live rocks will mean that you can have two systems helping each other and having something extra certainly doesn’t hurt at all.