When to start the timer on crock pot chicken confit

Generally speaking crock pot recipes require preheating the empty pot (for how long depends on the model, but it can be as much as half an hour, and usually on high even if cooking on low). This isn't included in the cooking time. Then the time normally starts when you put the food in, at the temperature specified in the recipe.

If you don't have time to fully preheat you can generally start with hot ingredients, and add the preheating time to the cooking time - the contents will cool at first, but not dangerously so. In this case, with the unusual process of starting low then turning on to high, I wouldn't do that.