I have the floss in the top as well, as the sponges do a pretty good job of removing most of the crud anyways. All that's left are the smaller particles that the floss will remove before going back to the tank.
Yes, the lava granules are another type of media like the ceramic rings and cylinders. But with the lava granules, you need to rinse off well before adding, as they can be very dusty. But they work great, and you never have to replace them. As for the ceramic rings, if you get a few rings that look clogged, you can either rinse them out or replace the clogged rings. It won't hurt the cycle, as if you replace, you'll just be replacing 2 or 3 rings out of a whole basket full. Personally, I would just use a tooth pick and poke through and then rinse the crud out so it's not clogged any more. But as long as I've been using them, still have no clogged rings, going on 10 months in my Emperor 280.