Padding would be good. Since she won't have a litter box at first and using one area might not happen, try putting some towels down and then fleece on top. You can set up a potty corner with litter if you want. Be careful with the litter you use so it doesn't irritate the incision, a paper based one might be best at first. A soft bed would be good as well. Any bedding should be easy to clean as well.
I know that dogs tend to recover pretty quickly. It can take a little while for them to figure out how to get around on 3 legs, but they do figure it out and tend to get around pretty well. Cats are similar I think and will even jumps up and down.
How you arrange things might depend on what leg is being amputated (I am not sure). A front leg might not be too much of an impact and she would probably get back to normal pretty quick. A back leg would be harder I think since they carry most of their weight on the back legs.
Also talk with your vet about it. While with a spay or neuter, you want to confine them for a week or 2, other surgeries might require the rabbit to move around more. They should also be able to give some advice on bedding and if she will be able to use a litter box right away or wait a bit.
