Hover your mouse over the tweet and move to the blank space on the right. One of the options should be to reply to that tweet. When you click reply, your box will automatically place an @username in the front. That person will know that you responded to them by checking their @replies in the right sidebar right above direct messages.
like AMFM explaning you can put an @ infront of the user you are answering to or send him a direct message if you are following him.