So would I put the vinyl down then a thin bit of straw everywhere apart from the litter box? In winter I would put more because of warmth.
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You would have vynil only everywhere, with no bedding on top. newspaper and lots of hay in the litter boxes. This gives the rabbits a clear distinction between what is a toilet area and not. You can sometimes get vynil offcuts from independent flooring shops for cheap or free, especially if you say it is for your rabbit hutch.