It will depend on the ingredient. Certain things, like some spices and dried peels etc should be boiled for a short time, like the last 5-10 minutes of the boil to extract their flavors and hydrate/sanitize them. Others, you're better off soaking in a neutral spirit like vodka and then adding the whole shebang to your secondary (vanilla beans and cacao nibs are good this way). Other stuff can just be dumped into secondary like sanitary fruit purees, or frozen fruit. Finally, things very strong in flavor like extracts and tinctures should probably be added at bottling to taste, dropwise to make sure you don't overdo it. It's probably best to ask about specific ingredients as you use them to get an idea of what the specific needs are.