I’ve had my Rex rabbit Sugar for about three years now. I got her from a Humane Society when she was about two years old; she had alreaded been spayed.
When I first got her, she would defacate and urinate on my bed and carpets. She would still use her litter box though. Due to this, I then got a loft bed and she very quickly stopped urinating on the carpets, however the defecations continued. Very recently I moved rooms (I’m in the same house just a different room) and I really want to stop her from taking a dump everywhere she goes, I also want to have my bed on the ground now. Does anyone know how I could prevent her from leaving a bitter present for me wherever she goes?
I’ve been putting her in her cage whenever she bestows me moist raisins and firmly telling her no and she’s bad, but that doesn’t seem to be doing much and it seems like she is pretty pissed at me now. Also, because her punishment is me putting her in her cage, it feels like she never gets any time to run around anymore.

What should I do about this? Is this a poor way to punish my rabbit? Are there other methods I should use? Should I just be patient and wait for it to work?

I really feel at a loss right now, I really don’t want to see Sugar’s poop everywhere, but I just don’t know how to stop her. She’s litter box trained and spayed- so I really don’t know what’s wrong except that she’s just marking her territory. I don’t wan’t her to mark her territory though- do I just need to show more dominance? How would I do that?
Any help would be great, thank you.