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In Mail.app on El Capitan, the Mailbox menu offers the menu item Use this mailbox as. A submenu offers the items Drafts Mailbox, Sent Mailbox, Junk Mailbox, Trash Mailbox, and Archive Mailbox.

After using one of these commands, the selected folder disappears. That folder's name is masked, displayed under the Drafts, Sent, Junk, Trash, and Archive icons at the top of the sidebar as the name of the account rather than the actual folder name.

How can I tell what is the currently designated folder for each function (Drafts, Sent, Junk, Trash, and Archive)?

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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.

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