The MAPI Connector employs the user WebMail (WebUser Interface) settings. It instructs the MAPI applications (such as the Microsoft Outlook) to use the same names for "Special" Mailboxes. As a result MAPI applications and the WebUser Interface use the same Trash or Deleted Items Mailbox to store removed messages, use the same Mailbox as the Main Calendar Mailbox, etc.
The MAPI Connector also retrieves the user Domain Mail Trailer setting. The content of that setting is added to all non-encrypted and not-signed text messages submitted via the MAPI Connector.
The values specified via the Account Settings panel are stored in the WebUser Settings, so both the WebUser Interface and MAPI sessions use the same From:, Reply-To:, and Organization values.