"I like to think chilis react like hops: They contribute different degrees of flavor and aroma, depending on when and how they are added to the batch.
Add the chilis to the bottle if you want the drinker to know it's there, and if you want the chili flavor to increase as the beer ages. The alcohol in the beer will leach out the hot and the fruity-spicy pepper flavor over time, and it won't get overly harsh. This will also give you a fair amount of hot peppery aroma. The ultimate in "dry-hopping"!
Alternatively, you could add the chilis to the wort during the last 5 minutes of the boil and continue to steep them in the wort for 15 minutes after shutting off the heat. This method will get the spicy flavor into the beer, like a late-boil flavor hop addition. Little aroma will remain, but this will contribute a solid, clean hot flavor if it's done with finesse.
A third possibility is to put the chilis into the primary fermenter as you pitch the yeast and leave them there until you rack to secondary. This will give you good heat, good pepper-as-fruit flavor, and enough chili aroma to balance the beer aromas. This is the method that adds the most to the beer's complexity. A fourth possibility is to add the chilis to the mash.
The pluses and minuses of these methods are worth considering: A bottle of beer with a chili in it is a statement, a challenge. A drawback, one best solved by using the second method above, is the sanitation question. Do you know where your chilis have been? Putting them into finished, fermented beer is probably safe, as the alcohol will likely kill off anything nasty. But 5 minutes of boiling and 15 minutes of steeping will do even better. "