
It doesn't matter to her where she goes, so she needs to learn that it isn't OK to pee indoors. If you cannot watch her every second then she needs confining to an area with a floor that is easy to clean until she gets the idea.
Often pups that have too much freedom within the house don't make the connection between the house being their denning area therefore to be kept clean. Carpet is more likely to retain her scent and encourage her to wee there again.
How old is she and are you still taking her outside and seeing her go, or relying on her going out herself. Remember most pups don't have real voluntary control until about 5 months so if distracted or too far from the place they are supposed to go they will simply have to go where they are.