Uninstall and reinstall SmarterMail. When you install, you specify the domain storage path.
If this doesn't appeal to you, open up your mailconfig.xml at C:\Program Files\SmarterTools\SmarterMail\Service.
Find the following block of configuration directives:
<!-- ** Path Settings ******************************* -->
<spoolPath>c:\SmarterMail\Spool\</spoolPath>
<rootMailPath>c:\SmarterMail\</rootMailPath>
<imapRetrievalDownloadPath>c:\SmarterMail\ImapRetrieval\</imapRetrievalDownloadPath>
<archivePath>c:\SmarterMail\Archive\</archivePath>
<logPath>c:\SmarterMail\Logs\</logPath>
<popRetrievalDownloadPath>c:\SmarterMail\PopRetrieval</popRetrievalDownloadPath>
Set the rootMailPath to your heart's content. Don't forget to restart the service.