I use the same kind of litter (Yesterday’s News), but I mainly just clean out the wet areas. I tilt the litter box, so it’s up on one end at about a 45 degree angle, and the clean dry pellets slide to the other end, then I scoop up all the wet litter that’s clinging in a clump on the high end. Then I reverse and scoop out the wet litter on the other end. I do this every day. I add more litter as necessary. Once a week or so, I dump out the entire contents and wash out the litter box with a natural/organic cleaner.
My two rabbits have free range of the house and screen porch and most of their poops, along with some of their pee, is on the carpet or floor, not in the litter box. I have 2 litter boxes in the house and 2 on the screen porch, but they mainly use one in each place (when they use it). I still find that the boxes need cleaning every day. I don’t like for my rabbits to sit in them, when they may be sitting on wetness.
With any method of cleaning, you are likely to waste some pellets that are still dry and clean, but that’s unavoidable.