No doubt soaking will leach some of the ammonia and urea out of the pellets, so I agree with HeyPK that keeping them damp rather than in water would more likely work well. The first time I used river silt as a lower level of my substrate I only soaked it for a few days, and only one time, then dumped the water and used the silt wet. My aquarium smelled very bad for a few days after I filled it, but the smell did go away. So, I assume I still had ammonia when I started using it.
Since you want to poke the pellets into the substrate, where they will be covered with the substrate, some ammonia and urea probably won't do any harm. The real problems show up if you later expose one of them to the water above the substrate. That is a great way to learn about green water and try out the many methods for getting rid of it.