They should be kept in a pen, especially when not supervised otherwise free run is OK if their area is rabbit proofed.
For their pen, something like a paneling with cotton fleece over it for a floor, this makes cleaning after them much easier.
Rabbits don't really litter train and not going running for the litter box to do their thing. In their home, they may go more in a litter box, but when that urge hits, they are going to piddle and poop where they are.
Installed carpets will soak urine and if not cleaned will get offensive over time, and means carpet cleaning,
defend liberty is the rabbit expert here, she can give better input and suggestions for house rabbits.
I had a pet skunk that took to the litter box, no worse than a cat really and never caged.
A pet possum, well, she didn't litter train too well, but cleaning after her was not such hard work.
She had her potty areas where she went most of the time, probably like a rabbit.