Most recipes lay it out for you, I get that, but if I were wanting to doctor up a recipe with an ingredient, how do I know where to add it?
Is there a rule of thumb for spices in the boil, fruits in the secondary, etc. etc.?
I have been brewing a great deal over the past year with spices, due to family members requesting spiced beers for events such as weddings and holidays. My thoughts on spices after all of this are as follows:
1. You can add your spices in three different ways. First, as boil additions (usually late additions, but not always). Second, as whole spices in secondary (or primary after fermentation is complete), left to steep until the desired level of flavor contribution is made. Don't use ground spices for this! And third, make a spice tea and add it at bottling/kegging time (see below).
2. A spice tea added with the priming solution at bottling or kegging gives you the most control, and really outperforms boil additions. Simply boil some water to sterilize it, then let your spices steep in the hot water for awhile. I just put them in and leave. By the time I come back later, the water has usually cooled (although hopefully you have a pot that is insulated well enough to keep the heat for awhile) and I have an intensely spiced tea that I can add to the beer in measured amounts to taste.
3. Boil timing totally depends on the spice. If you're adding spices to the boil, you need to know your individual spices and how they perform before using them. Nutmeg added in small quantities in the boil at 5 minutes will be discernible in the final beer, whereas star anise added at the same time will smell overpowering going into the fermentor, but will be all but undetectable after fermentation. Instead, to be used in the boil, it needs to be added for a longer period of time. Know your spices! (It helps if you cook).
4. The previous rule also applies to quantities, regardless of when you are adding the spices. Some spices are much more potent than others. In this case, the above examples (nutmeg and star anise) must both be carefully moderated, as they are very pungent and can mute other flavors, while something like citrus peel tends to be a bit more forgiving when added in larger quantities.
5. When working with less familiar spices, feel free (in fact, encouraged) to experiment. However, it almost always helps to make a small quantity of tea with the spice to see what it will taste like in liquid. I did a wheat beer with sweet orange peel and pink peppercorns a few months ago. I did not make a tea, and I was very surprised at what the pink peppercorns tasted like in the beer. It was recognisable and it wasn't bad, but it wasn't what I expected.
Hopefully this helps, at least on the spice end of your question. This is by no means a rulebook, and every spice is different, but if you follow these guidelines and experiment, you will at least be on the right track, I think.
