If you scoop out the faeces (and any soiled pellets) daily and stir the pellets in the top tray, these pellets need only be topped up and will not need to be replaced, in principle. There will always be exceptions of course, for example, if your cat has diarrhoea.
The bottom tray should be emptied about once a week, or more often if used by several cats or when the bottom tray is full of sawdust. If the bottom tray is too full, the system will no longer work and the soiled pellets will remain in the top tray, causing it to smell.
The bottom tray can be cleaned using a soft cloth with a mild soap solution or hot water with vinegar or baking soda. Or simply rinse under the tap. Do not use scourers or abrasives. These will leave tiny scratches, which are a breeding ground for bacteria and can cause smells.