Not really an answer, but since I think it's good that people have easy access to all the information available, on meta.SO you can find more than you ever wanted to know about how comment replies work:
How do comment @replies work?
Update: As of 1 July 2011 there's a major change in @replies: If there are comments on a post already, and I start my comment with "@postowner, @othercommenter", then the "@postowner" will no longer block othercommenter to be notified of my comment. See #8 of How do comment @replies work?
On a related note, if there are no other commenters, then "@postower" will be stripped from my comment.
Here I leave what I previously wrote; it's totally obsolete now, but helps understanding the extensive discussion on the subject in April 2011.
Here's what I do if I want to notify both someone who commented on a post and the author of that post: Say Bob wrote an answer, and Alice commented on that answer. Then my comment would start, e.g., with
@Alice, @Bob: Just to let you know ...
(Note that the order is important here; "@Bob, @Alice" wouldn't work!)
Why do I write it like that? The "@Alice" is to notify Alice, and Bob is notified anyway since he's the author of the post (i.e., the answer). The only reason for writing "@Bob" is to make it clear to Bob (and others) that this comment is also addressed at him, not only at Alice. (This is useful if there's a long comment thread already and Bob is drowning in all the notifications, and it's also a pointer for other people reading the comments.)