I have 3 bunnies that stay indoors :o)
You can buy plastic wire protectors from B&Q or similar, but still keep an eye on them as they can still chew through that given half a chance.
Despite what many people think, they're clean animals and don't really like to do their business just anywhere, they usually have a self appointed spot, once you know where that spot is, get a cat litter trat and put it in that spot. They might think it a bit odd and poo somewhere else to start with, but percevere (sp?) and put their droppings in the tray and they soon catch on they're to do it directly in the tray. This makes life easier for you.
They will have a toilet area in their hutch, I don't use the tray in their hutch as they kept tipping it over, so now I just clean out their toilet area every other day, and this ensures there no smell in your house.
At Pets At Home (probably other pet stores too), you can get 'cage fresh granuals'. Sprinkle that down in their toilet area and that soaks up smells too - it smells like baby powder LOL.
This is the hutch I keep my 3 in
http://www.petsathome.com/find/keyword-is-rabb it+hutch/product-is-13200 they like to be in the private area when they're sleeping (or in a grump) and the rest of the top floor I have their feeding bowls and water bottle.
Bunnies are fond of knocking food bowls over so I have a couple of bowls that attach to the bars. This is it
http://www.opentip.com/product_info.php?ref=89 55&products_id=675404&affiliate_banner_id=1 you get all different shapes and materials, try not to go for a plastic one though as they do nibble on it.
I let them out every night as soon as I