The way my bun's cage and litter box are set up helps me keep his habitat clean-
I know i'm not getting really positive feedback when admitting that my bun's litterbox area is soft coated mesh(all other areas of his cage are covered with soft floorboards) and that most his droppings ( he sometimes tosses them around with hay) and all his pee fall straight down into a big plastic lidless box lined with a trash bag and hay in the bottom, at the top and between some layers of waste(note that his cage sits above ground on a wooden frame, lined with plastic bags to prevent rot in mesh-only area)
When it's cleaning time, i let my bunny roam, then i kick out the dust from the floorboard, clean out hay from the mesh, tie up the trashbag and dump the organic waste in the correct bin, doing same with the bag, clean out the box walls when needed, set up the cage floor, waste-box and the interior, replacing anything broken or empty.
Keeps the place clean and free of stink!