You can train a rabbit to go in a litterbox just like a cat. I did it with all my rabbits. It isn't even that difficult to do. They naturally want to poop in one place already, so it's just a matter of getting them used to the idea of a box.
You can also get your rabbits fixed. Most humane societies will do it for free when you get the rabbit.
The biggest issue I've found is they love to chew through computer cords when given the run of the house. However, there's cord protectors you can get to wrap around your power cords and they won't bother once that's done. Also, if they get plenty of chewing toys, they'll leave your stuff alone (my last rabbit adored pushing around and chewing this little wooden car we got him). They also really like the cat toys with a spring and a fuzzle on the end.