I keg my beer, so I normally add it to the bottom of the keg and rack on top of it. Works very well. However, if you're bottling, I don't know if it'll affect carbonation by draging the yeast out of suspension before it's done its job.
Edit: Actually, I just thought about it for a second and if that were the case, you couldn't use it in the primary/secondary anyway. Just mix it in the same solution as your priming sugar and you should be fine.