I've had bunnies for over 10 years now.
When you get well-socialized, tame bunnies they are quite bossy little critters, and they're blunt. When they meet someone new (rabbit, person, dog, cat) they just run over and decide whether it should be fought, humped, used for pets or treats etc. When they get hyper they run around and "binky" which is pretty cute.
They love to rearrange stuff... throwing stuff around, chewing it, pushing it out of the way, digging it etc. Assuming you keep them inside, all of your wires have to be encased in something like PVC because they treat wires like brambles and chew them to get them out of the way. With some bunnies, you let them in an un-bunny-proofed room and they literally head straight for the wires (RIP ethernet). Sometimes they will rearrange you if you are in their space (dig at you, nibble on your clothes, shove your hand out of the way with their head etc.). They also eat books, most of my favorite books (which were always lying around) from the period I had house rabbits have parts of the cover eaten.
Some rabbits are naturally tidy and will only go in one corner, some **** all over the place. Most pee in one place. What I've done is kept them on full bedding for a week or two, then put some used bedding in a litterbox in the corner they go in and newspaper in the rest of the cage. They are more inclined to do their business on a familiar texture/smell. The hayrack should also go above the litterbox because they tend to poo when they eat. They might still poo all over the cage, but that doesn't mean they can't be housetrained outside of cage. It works best to have their cage where you exercise them... then basically like training other animals, you have to try to predict when they're about to go on your floor, shoo them back to the litterbox and reward. I never clicker trained but I'm sure that would work. Sometimes they'll pee in a corner no matter what you do, if that happens just put a litterbox down there and live with it lol. And FWIW I've never checked it out scientifically but I'm pretty sure their pee is especially caustic, so be careful of what they can pee on. They tend to back up and lift up their butt when they pee, so you have to be careful they aren't peeing over the edge of the litterbox.
Males especially have to be neutered if you want to keep them inside as they will leap and pee at the same time to spray urine all over the place. I tolerate gross stuff better than 95% of people I know but a wash of bunny pee to the face is pretty nasty lol. Be careful choosing a bunny vet as they dont' handle anesthesia very well. Ask how many bunnies they lose... one vet told me he loses 10%. It should not be 10%!!
This organization has lots of info for keeping house rabbits, here is their section on house training:
http://rabbit.org/category/care/litter-training-care/