When you add fruit, your two concerns are sanitation and flavor.
Adding fruit to the boil guarantees that it will be sanitary, if you leave it in for long enough. Doing so, however, will volatolize off most of the flavor.
Adding fruit to the primary is a little better, but the active yeast will scrub a lot of the fruit flavors out of the beer and, because the beer is still alcohol free, it's a GREAT environment for wild-yeast and bacteria. That means that sanitation is a must for fruit added in primary.
Adding fruit after fermentation has ended is a better alternative. The yeast is less active, so it's not scrubbing out flavor. The beer already has alcohol in solution, so wild-yeast and bacteria growth is slowed. I still think that sanitation is important, but you don't have to worry yourself sick.
Hopsalot writes that because the cherries he uses are frozen, "the cell walls are broken allowing flavor to pour into your beer." I've heard this before, but can't speak for it myself: I'm not sure why the organelles of a cherry cell would taste better than the cell-wall. . . but it's definitely something that's been floating around a lot, so I can't disagree.
He also writes that his cherries "are sanitzed due to being frozen". I think he means that because they are commercially packaged, he's comfortable assuming they are pre-sanitized. I agree that that's a safe bet, but I like to stun the bacteria with a quick boil and then a sudden chill. Why take a chance if it's something you're looking forward to? In any event, to be clear: just freezing the cherries will NOT sanitize them.
Something I've wondered about is using a sous-vide bag to boil the cherries - that way they wouldn't get wet even when they were being heated. I guess throwing them in the oven would do the same thing. . . but the bag just feels sanitary-er to me. So that's another thought.
Same deal goes for the chocolate as for the cherries: sanitation/flavor.