They have turf on the ground under their cage and bedding material in 2 litter boxes in the cage. One upstairs and one downstairs. I’ve started putting her food in the box and it’s helping some. At this point I don’t let her freely roam the house like my adult bunny does (he is house broken) I bring her out and watch her roam for about 30 min at a time and then put her back in her home. Her cage stays open during the day, but she won’t freely leave it yet like my Bennie does.Does the cage have bedding in it everywhere? If it does I'd take the bedding out and put bedding in the litterbox. Rabbits don't like to pee on hard surfaces where it could get their butts wet so they'll typically go to the bedding. Putting food where they have to sit in the litterbox helps too. Then when she's consistently using the litter box you can start laying down some fleece in the cage (or slowly introducing carpeted areas if she's a "roamer"). If she's going to roam I'd introduce the spaces very slowly so she doesn't get all happy go lucky and pee everywhere on your carpet.
Try wiping up pee and puting it in the litter box. That way, they think that's were they marked their territory.