Take a look at the habitats the forum users here https://binkybunny.com/BUNNYINFO/GreatHabitats/tabid/229/Default.aspx
This is a houserabbit site so if your bunny isn’t inside, bring her in!
The hutch you describe isn’t big enough, especially if your bunny is in there all the time. I know they sell these hutches for bunnies, but they are a remnant from when rabbits were kept in the back garden for meat, so quality of life was not an issue and no one knew what bunnies were even like. They have lots of energy and need lots of space just like cats!
Second levels like that don’t count for floor space and things like the ramp take out much of the space on both the top and bottom for being viable. Not being able to put the litter tray on the top floor is a massive clue that it isn’t big enough.
I had a similar hutch because I was also ill informed when I got my first bunny, so I attached a dog exercise pen to the front of it (about £30, with a roll of linoleum for the floor) so my bunny could have a home base in the hutch, but also plenty of space to stretch and run (and also house his toys, boxes and litter tray) in the pen. Litter habits tend to improve when the bunny has a happier space to live in, and being able to come and go as they please from their house to their exercise area is a massive plus (just by opening the pen up to the rest of the room) Always picking up the bunny to remove them from the hutch can be very scary for them.
I hope you find some inspiration in the habitats section, please let us know how you get on!