The smell is the worst. My husband's tortie cat was peeing under our bed at our old house. Took me a couple of weeks to find it and it was right where the floor joins the wall so the pee was up under the wall trim and everything. I had to take our bed apart and take it out of the room to be able to get to it all. We slept in the living room for a couple of weeks. I cleaned the carpet at least a dozen times and used a half gallon of vinegar, soaking it into the padding and letting it dry.
I would definitely put a box in the bedroom just in case. Even if it's a plastic tub turned into a box so the baby can't get into it as easily.
That picture of him with your son is adorable!!