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In the cage Tofu is a perfect gentleman when it comes to using his litter box for peeing. He poops in there, but still poops all over the cage (territorial poop?)
Out of the cage Tofu doesn't know what to do. I have a pen set up around his cage since I can't free range him yet without him pooping everywhere (1 week until the month mark for his neuter!)
I've started putting his litter box inside the pen because otherwise he will just pee on the carpet. I don't know why though, since he will hop in and out of his cage all day but he won't use the litter box when he's allowed out in the pen. I even put the litterbox over the spot he seemed to pick for the bathroom, but he just pees somewhere else or around it. very frustrating.
Sometimes he won't territory poop all day. Then i'll look over and there will be a dozen little pills all over the place. He still sprays on the porch. hmph.
Rupert used to do the same thing too, I think it's just that when they're in cages they figure that's the only place they can go and not foul up their other space so they use it, but once outside it's fair game. What I did was brace myself for accidents and let him out into the pen anyway, put one box down in a corner with hay and litter, and cleaned up any accidents outside of the box. Once I figured that he liked to use that whole corner I put down another box and left it like that for about 2 weeks -- I never had any accidents after I put the second box down. I have since removed one of the boxes and he's been very good about going more or less only in the box (peeing anyway) and not where the other box used to be. Good luck!