Identify which folder on mail server is currently designated by Mail.app as Drafts, Junk, Trash, Sent, Archive
You can read it with a text editor at the beginning of the file ~/Library/Mail/V3/MailData/BackupTOC.plist. 

While you can read the paths of the mailboxes, you do not see, which belongs to Drafts and which to Sent, etc. On my system, the entries in the file are in the following order: Inbox, Drafts, Sent, Trash, Junk, Archive.

The mailboxes for each account are listed next to each other. 

Note: Changes to the paths in this file have no effect. You must set it within the Mail application.