I agree that there should be a litterbox on each level of your house (one upstairs one downstairs). As long as he gets a clean check from your vet first, I would add another litterbox.

As emily_the_spoiled said, make sure you clean the areas that he urinated very well with enzyme cleaner. Also, he may have done it somewhere else when you haven't seen him. If you buy a black light, this will pick up any areas that you missed.

Good Luck!