There is really isn’t much you can do but limit his space for now. His instinct -especially in the coming weeks when his hormones rise- is to mark everywhere. I suggest setting up either an exercise pen or allowing him in a smaller space/room where you can sweep the floor after he’s has poop-bombed it. I know it’s harder to hang out with them when they’re penned up…
It’s only temporary, as the litter habits improve & they get a bit older, they can have more access to roaming space again.
If you plan to keep him as your only rabbit, neutering isn’t absolutely necessary for a male rabbit but it can help with hormonal behaviours, so it’s definitely something to consider.
Are you placing hay on the litterboxes he has? They tend to do a lot of their poops when they’re sitting in the box eating hay. That might help him deposit most of them there… but baby bunnies are poop machines, so no promises!