I don’t think it’s going to confuse her. I also have two litter boxes for my bunny, one outside her cage and one inside.But, I would normally find her using the one outside (she likes it better).

I have underbed storage boxes lined with newspaper, half a puppy training pad and then half filled with hay. I didn’t have this for my first bunny, just a cat litter tray, and she was difficult to litter train. I started using boxes in every corner with my second and third bunnies. My recent three are all rescues, one who can’t be neutered on health grounds, and they all started using the hay boxes straight away. It sounds like your little girl is happy with just the one, but I would at least pop one more in, maybe at the top? Numerous ones become more important if bunny has time out and access to large floor areas.

We have a two story cage for our two bunnies, brother and sister. In the beginning they had two toilets in both their cage and playpen but now we only put in one. They also have one on the bottom level of their cage cause they always shove eveything off the top layer for some reason (even the plastic toilet tray) and like to lay right on the plastic floor. I find they use their hey feeders and water the most at the top as well. The upper layer has become their snuggle and eat area most of the time and the bottom layer is more toilet and play. I find it funny how they set that up. To be honest they have not been using an indoor playpen for a while because it is warm enough to build it outside (Where I am not sure there is a need for a special toilet?) and also because my little boy bunny learned how to jump right out of the playpen and started doing so so often that we couldnt have them out anymore unless someone was going to be sitting right there watching them. I will have to figure out something new for next aumtun/winter unless he has calmed down with the jumping by then. Currently my little girl is 6 months old and has not yet been spayed. We are going to be talking to the vet soon about getting this done and our options here in Germany. She has some mood issues happening here at times (but then again she was always a bit more standoffish than her brother) but she has not been having any trouble with her pee thankfully and they both seem to use the toilet the majority of the time.

When I just had Bandit, he only had one litter tray on the bottom level of his cage (two level). When he was let out he had access to multiple rooms and would always return to his cage to use the box, except for a couple stray poops here and there which is to be expected.