When they are just starting to train I start by putting a box in each corner of their area. Then I watch them and see which one they are using the most. In some cases they don't use any of the ones I have given them and they pick their own spot. (They usually pick their own spot and once they start peeing there that is usually the spot they return too, as they now have their scent laid there) Once they pick their spot I move a liter box over that spot, and the ones I have put out I check. If they are using it I leave it. If they aren't I take them out. After time they work down to just one or two. It's just trial and error. Most rabbits I find pretty much train themselves as long as you pay attention to where they are going and follow their lead.
I did have one rabbit that would NEVER go in a liter box. She was not spayed. I tried every type of liter box and she would literally take any box I gave her and dump it out and spread all the bedding over her entire area. She had a large cage in her area so I ended up just putting bedding down on the bottom and putting her hay manger in there. She just used the entire cage bottom as her liter box, and she could sit in there and eat hay. It was just a big liter box to her. She never peed any where outside of it though. She would just not commit herself to one box and instead used one area which ended up being OK. It just cost me more in bedding as I was having to bed the whole cage bottom. I would try to keep up with her though and just scoop out the area she used each day and replace with clean bedding. It was just her thing I guess. She was the only one I ever had an issue with not using a liter box.