Mail Archiver handles duplicate mails automatically. You don't need to do anything.
The message-id identifies a mail
Each mail has a universally unique identifier called message-id. You can see the message-id when you look at the header of a mail. Here is a message-id from my ticket system:
Universally unique means that there is only one mail with this identifier ever. Mail Archiver reads the message-id and checks the id against the ids in the archive.
"But I get so many duplicates in Mail"
AppleMail is a very special app and saves many duplicate mails. Again Mail Archiver checks the message-id of the mails it reads against the database and skips the duplicate mails.
Exceptions for having message-ids in a mail
Every rule has an exception. Spammers like to be creative. I have a couple of mails without messages-ids. I've also seen mails from self-written mail systems where the developers have forgotten the message-ids. When Mail Archiver doesn't find a message-id it makes a fingerprint of the mail from From, To, the Subject and the date of the mail.