Litter training??

First question, are both rabbits spayed/neutered? If you male isn't neutered yet, it's usually harder to train unneutered males. I have both a male and a female that are litter trained. Both occasionally poop outside the litterbox, but rarely pee outside of it (sometimes the male does if he's far from it now because he is 13 years old and apparently doesn't always remember to go find the litterbox). If you're currently giving them the run of the place and you just got them, they can mark territory with poops. So this behavior may calm down. I would suggest starting off giving him only a small area, say about 16 square feet or so. Not less than 8 square feet. And once he does fine in that area, he should do fine in the rest of the house (more than one litterbox may be necessary in a large house). Hope that helps!