smart mailboxes

If I arrange a smart mailbox to store all emails from a specific organisation, and I answer an email from that organisation, is the email updated in the smart mailbox and the original mailbox? Reading these threads, I cannot understand why the smart mailbox keeps copies of the email, and not just the email itself. I am in the position of having several smart mailboxes and several incarnations of the same email, making it hard to control them, and remember if I have answered them. If I delete an email, or reply to one, is it deleted or updated across the whole email system?