If he's good with his litter box in his cage, and usually only leaves pellets outside the cage, it's likely that he knows how to use the box just fine and is just using pellets to mark his teritory.
How long have you had him for in the area he's in now? I know when I bring my bunnies to new places, or even to new areas of the house, they'll leave droppings around to mark the teritory.
Maybe you can read up on litter box training and try using a second one outside of the cage. But that doesn't always help for rabbits who are marking.
Are you planning on bonding the two rabbits once the female is spayed? Because while bonding my rabbits, I noticed that at first they would mark more, but after they were fully bonded and lived in the same cage together they both got much better. They hardly ever go to the bathroom outside of the litter box now.
But to answer your questions, he may still mark even if he is fixed (and even if the female is fixed too), if he can smell an "intruder". It may decrease more as his testerone drops, but I wouldn't be to suprised if he continued it either. Even if you pet her, then go into his area, that could be carrying her smell to him. If your planning on bonding them, I would set up their two cages next to each other so they can see and smell each other for awhile without being able to directly interact. He'll probably mark more at first, but as they get more use to each other and he learns that she is a friend rather than an intruder, the marking should decrease.
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