Sorry I am back. I think for the first 4 months of my little sweet pea's life she had HORRIBLE litter habbits. meaning none at all. Not sure how long the training process is supossed to take.
I have been putting ALL the hay in the box, which she sits in all the time, and actually leaves to do her business. So I took notice of where she seems to like to go (planning on moving her box there.) But its EVERYWHERE other than the box. it looks like she pees all over the left side of the cage, and poops all in the middle.
Is that typical? I thought they would tend to go in the same spot?
I just went out and got a second litter box last night to put on the left side, and she did use it last night, not exclusivly but its a start and i will take it.
Sorry for the novel.

Typically young adolescent bunnies may pee everywhere. Have you considered having her spayed? She's about the age that some vets do it. (Here it's 6 months). I strongly reccommend having it done bc it should double her lifespan and improve her behaviors - particularly in the litter box department!

Acacia was litter trained a little bit before she was done but since she has been perfect EXCEPT when there were threats around. Before she got used to my dog/cats when I moved back home she would pee along the perimeter of her enclosure. Also, during separate free runs, both my female bunnies (un-bonded) would pee along the baby gate to establish their territory and dominance. So is there any threats from other animals that could be encouraging her to feel threatened?
Also, The cage litter (I assume you have a cage, if not whatever you're covering the bottom with) needs to be different than the box litter. Some people use kiln dried or aspen shaving s in their commercial cages but also in the litter box, this means she doesn't differentiate the two- regardless of the hay and litter box. My bunny has plain sheets of newspaper in her box to pee on while the bottom of her pen is carpet and all the levels are only lined with newspaper but topped with blankets.

But, you're doing good with the hay feeding in the litter box!!
Hope this helps!

I agree with Purple-Hops, most bunnies can't be fully litter-trained until they're spayed adults.

What kind of litterbox are you using? It's good that you got a second one, I was going to recommend that . I once adopted two neutered males who weren't trained at all. I had to put a litterbox in every corner of the cage and slowly reduce the number of boxes over time.