No she is not spayed I'm to scared to take the risk because I know some people have lost their bunnys having them spayed.It's great that she's peeing in the litter box, because that's the biggest hassle to clean, haha!
To start, it's almost impossible for a rabbit to go 100% in the litter box all the time. Pooping, with how frequently they do it, is going to happen at least occasionally out of the box. Rabbits tend to do their business in a designated spot (in which case, we place a litter box), but they aren't necessarily wired to path to that toilet every time they need to go.
If she is not spayed, the pooping is most likely territorial -- she's marking her territory so she feels more secure. Unfortunately, this is a natural instinct that can't really be trained out of a rabbit.
Is she spayed?