Per this blog post this is how to Auto Filer in iManage Emm Toolbar is supposed to work

When an e-mail is filed into a workspace, a tag is added to the subject line of the e-mail in brackets. The format of the Subject Tag is
<Original Subject> [<Firm ID>-<Database>.<Folder ID>].
The format and position of the Subject Tag can be customized by modifying registry keys. Refer to the WorkSite Desktop Client Customization Guide for more
information.

When an e-mail that you have sent and filed using E-mail Management is returned to you (for example, someone replied to your e-mail), it is flagged in the Inbox to
indicate that the e-mail has been automatically filed to the same WorkSite folder as the original.
An Inbox Filer checks the Subject Tag of each new e-mail in the Inbox. If the format of the Subject Tag is correct, the Inbox Filer checks whether the e-mail is
filed. If the e-mail is filed, the filer marks it as filed. If the e-mail is not filed, the Inbox Filer files the e-mail to the appropriate location, and then marks it as filed.

To enable this you need to have the following Registry Keys

HKEY_CURRENT_USER\Software\Interwoven\WorkSite\8.0\EMM\Config

This is the Client Side Inbox Filer

DisableInboxFiler : False ( String )

This is the Client Side Sent Items Filer

DisableSentFiler : False ( String )