Start with a smaller area, like a playpen. When he does well in the playpen, enlarge his area. When he does well in that area, you can give him more space. Rabbits mark their area with their poop, so he might always leave some poop, but he should get better.
If he is just three months old, they are territorial markings. There will always be some poop on the floor until you get him neutered. However, one way to make him poop in his litter box a bit more is to put lots of hay in it. Also, if you want, you can put his food bowl at the end if his litter box beside his hay. Rabbits tend to poop/pee more when they are eating in their litter box. I don’t know if you want to do it this way, but I’ve had my bun for a while, and it works nice. I can post a picture if you’d like. Also, if he starts to poop a lot everywhere, place him in his litter box for a bit and see if he poops in it. If he does, praise him and let him to show him pooping in the litter box was good. Below is the way my litter box is set up.