I know this isn't what you asked, but I wanted to say that I think the super pet large cage is too small for a rabbit. A minimum size should be 2'x4' - that's the size of the biggest super pet cage (the giant I think?). My second rabbit was kept in the large cage and it was really too small for her. With rabbits, more room is better to avoid bad habits - the more room they have to expend energy, the less they'll chew on bars, dig, etc.
To answer your question, you would just put litter in the box and then you can leave the floor bare or put down fleece or something. When the bunny is new you'll probably want to leave it bare to help litter training, but you can add a blanket in once you know the bunny won't pee on it.