Mine were fairly good before, but after the boys were castrated and the girls were spayed I had no problems with them. Wees are 100% in the litter tray, you will probably always find the odd poo but that might be from kicking it out of the litter tray or sheer excitement.. I have always filled the litter trays with hay and also keep hay in hay racks etc around the litter tray so it encourages them to toilet there.
When rabbits are neutered their hormones will die down (may take a few days/weeks) so they won't feel the need to mark everywhere, which is what your rabbit is doing.