The Archive mailbox is a place to put old emails. Not sure it's a good idea to put the actual mailbox folders in the /Home/Library/Mail/ folder. It's possible to export an entire mailbox or use third-party software to archive mail in a searchable database.
If you wish to retain mail and mailboxes in Mail then you only need Copy mail to the Archive folder rather than Move it. If retaining all of your mail in their assigned mailboxes then don't do anything with them, thus leaving the Archive mailbox empty. Whatever mailbox folders you have put in the Archive mailbox I would put them back where you had them unless you Copied them and did not Move them. If you Copied then you can safely delete the copies in your Archive mailbox.