Unneutered rabbits have difficulty adapting to life in a human household. You should see an improvement in housetraining within 2-3 weeks of having your male bunny neutered. With females, the behavioral benefits may take several months to be noticeable. The more time your rabbit spends in a plastic tray filled with rabbit-safe litter, the more accustomed to using a box he will become. It doesn't matter whether he's actually eliminating in the box or simply sitting in it.
Many rabbits even sleep in their litterbox.
Conversely, every time he eliminates outside a litterbox, that behavior is becoming habitual. This is why prevention, through supervision and confinement, plays such a major role in training. Less running area while she's in training, that is. Free-run time for a rabbit who is not yet housetrained should be limited to a single room that is plentifully supplied with litterboxes. Once again you are setting her up to succeed by putting her in a situation where it's easy for her to do what you want her to do.