Hi Kristi,
Sorry for the late reply. I would do what you are doing, keep the heating pad in the box, but make sure there is enough room for them to move off of it. You might even lower the temp of it a bit to see if they will stay on it longer. As long as they are not chilly, they are ok. If they are choosing to move away from the heat, I see nothing wrong with this, especially since the room has no drafts and is warm as well. We let our pups make that decision for themselves too, our heating pad takes up half of the whelping box and it gives them the choice of staying on it or moving away from the heat.
Hope this helps, where are the pics of those youngsters????
