I add it in after they're cooked, along with cinnamon and flaxseed. It would be interesting to see what boiling the peanut butter would do though. Never thought of trying it.

I am not the parent, but I have found that adding it while it is boiling reduces the risk of lumps being left behind once I start reaching into the very bottom of the peanut butter jar (I buy PB in 1kg jars and if I'm not diligent about stirring it now and then it becomes hard in the bottom).