It’s normal for buns to mark their territory when they enter a new environment. Two weeks doesn’t sound that long to be in your home so he could still be marking. On top of that, sometimes it can take more than five weeks for hormones to die down post-neuter, so that could also be a reason.
Have you been actively training him to go do his business in the litter box? Try limiting his space in a pen for now until he gets litter trained. He will most likely choose a favourite spot to pee, so put the litter box in that spot. If he pees anywhere else, soak it up with a paper towel and toss it in the box. Then wipe the area with a vinegar + water solution to rid of the smell. Toss stray poops into the box as well.
I recommend getting non-clumping wood pellets instead of newspaper for litter. Newspaper gets pretty icky when it’s wet and could also cause their feet to become stained. The hay doesn’t do much to help absorb pee. You could use the non-clumping pellets for your cats’ litter boxes too
Don’t use clumping litter because it’s dangerous if the bunny ingests it.
Bunnies like to eat and pee/poop at the same time, so a lot of us put their hay in the box or in a hay rack beside it.