So long as you start the tweet with @[twitteruser], your @reply will only appear in someone's feed if they follow you and also the person you are sending the at-reply to. Or if they are the person you're sending the message to, of course.
1) They are the user you are sending the @reply to, OR 2) They follow you AND the person you send the @reply to.
So for example, if I follow @balsamiq and @fogbugz and @balsamiq sends an @reply to @fogbugz, that message will appear in my feed. But if @balsamiq sends an @reply to a user I do not follow, I will not see it in my feed.