Definitely the neuter situation is the first thing to ask. Bunnies are much more prone to litterboxes once they’ve been fixed. But it’s also important to mention that 2 weeks is not really very much time to have had your bun, either. Bunnies often take quite a lot of time to get fully comfortable with their environment, and with you! Pooping everywhere is a sign of territorial marking.
If he’s unfixed, consider getting him neutered as soon as possible. After that or if you decide not to do that (it’s highly recommended that you do), what you can try is slowly letting him get used to his environment. Keep him in his enclosure for a while, letting him get fully used to the space and to “chin” and mark as he will so that he knows that that is his space. Try to avoid cleaning or reaching inside his enclosure while he’s inside – this will make him feel more insecure about his space, as would a giant foreign hand dropping into your living room would make you feel insecure!
Continue as you have been by picking up after him and placing the waste inside the box. Then, slowly expand his world and allow him to explore other areas. You may still find for the first month or two that he is continuing to do territorial marks, but this should eventually go away, especially when/if he gets fixed. 