As for when/how much to add, it depends on the recipe and what you're going for. In my ginger ale, for example, I add some ginger to the boil and some to the primary/secondary, so I get a combination of the ginger-y heat and bite, along with the aroma and flavor.
As for sanitation, adding at the last few minutes of the boil will effectively sanitize anything. When adding to the primary/secondary, I will use a variety of methods depending on what I'm sanitizing and my mood that day:
- Boil the addition in some water for a few minutes
- If it's something I don't want to boil (because it might bitter or ruin the flavor), hold them in some water at a high temperature (180ish) for some time - i.e. pasteurize them
- Soak the item in high-proof spirits, then add the spirits and all to the fermenter. This is the route I usually take with oak chips/cubes. I find bourbon is great for this.
I'd probably go the pasteurization route for orange zest. For things like powdered spices and chocolate, I usually just toss them right in.
As for nutmeg, I would definitely grate it before adding.