A cage won't stay 'nice', unfortunately - rabbits make a mess, there is hay everywhere all the time and they will move things around, that's a given. And the most time your rabbit will spend in it, the more he will move things around and make a mess (how big is it? How many hours a day is he out of it?). If it's not the case, I suggest you put litter (wood pellet litter, no shavings which always make a terrible mess and can be bad for the rabbit) in a litter box inside the cage and don't put anything on the bottom of the cage itself.
You've only had the rabbit for a week. You have to let him settle down, especially since it's a petshop bunny (so incorrect diet and sociabilisation are almost a given). But if I were you I would take this rabbit for a vet check-up quickly because I would be afraid of dental problems. You will probably have to transition to a better brand of pellets and you'll need to introduce vegetables one by one slowly, as rabbits in petshops are badly fed and born from rabbits who don't have a correct diet either which often makes it harder for them to digest things. But the most important thing is for your rabbit to eat tons of hay. Go to the website stevesmum gave you, it's reliable and very complete - everyone owning a rabbit should read it.
