Is she a baby bunny? It is sometimes not easy to litter box train a rabbit that hasn’t been spayed or neutered, so you might not have a lot of luck with that if she isn’t spayed yet. Keep putting poops in her litter box that you find, along with bits of paper towels that you have used to soak up any pee in other places. Then clean the other places she is peeing in with a white vinegar and water solution to hopefully take away the pee smell that might entice her to pee there again.
That cage looks small. Most cages that are sold in pet stores are not at all an adequate size for rabbits. A little bunny might not need as much space, but they grow quickly. One minimum suggested size for a cage is 2 feet by 4 feet, or sometimes the suggestions say that the cage should be 4 times the size of your bunny, but they will still need a certain number of hours outside the cage for exercise (in a bunny proofed room).
The BUNNY INFO link at the top left of the page has a lot of good information about the basics of rabbit care, including housing.