Bio wheels should never need to be replaced unless they become damaged. If the outflow is slow, it will cause your bio wheels to slow or stop all together. Clean the area where the bio wheel pegs sit, clean the area where the bio wheel turns. Keep your filter media rinsed out so it does not become clogged and reduce the flow so much the bio wheels stop turning. As long as the bio wheel turns enough to stay moist, its doing its drop, it does not have to turn fast, it just has to stay wet.
As far as the rocks, remove them and replace with filter cartridges, or filter material. Don't remove it all at one time or your tank will have a mini cycle. I suggest removeing one side at the time.