Do they have at least two litterboxes? She may not want to use the same one he is using, as it belongs to him, which is why she is using the floor.

How long have you had her? How did you go about introducing them?

It sounds like you need to be able to feed them separately, to make sure he gets enough, and she doesn't get too much.

How big is their "room," and do they each have places to climb and or hide when they want to be away from each other?