The easiest way to keep your rabbit hutch floors clean is to do a spot clean every day and a full clean out once a week. Brush out the hutch with a brush and dustpan then sprinkle a disinfectant powder onto the clean surface. Then cover with a thick wad of newspaper, these are extremely useful as the printers ink deters mites as they do not like it. Cover with a layer of woodshavings or straw.
To dispose of hutch waste you could roll it up and burn it in a small garden incinerator or dispose of it in your council bin for green waste as it will make lovely compost.
Every month or so the hutch will need a thorough scrub out to get rid of urine build up. There are lots of sprays on the market or you could use diluted Jeyes fluid or Virkon. Doing this prevents odour aswell as being a great fly deterrent.
Rabbits can be trained to use a litter tray in their homes, start by putting it in the toilet corner they usually use and put some droppings into it. They will soon get the idea and are creatures of habit so will happily return to the same place, making it much easier for you to keep the hutch clean.