How will Quest Migration Manager handle pre-existing mailboxes depends on the Exchange version that is holding the preexisting mailboxes.
1. For Exchange versions up to and including Exchange 2010 mailboxes must be deleted off the target for Migration Manager to sync source mailboxes.
To automate deletion of preexisting mailboxes please view the following video.
The following discusses using the "ForbidDelMailbox2010" option to delete prexisting mailboxes.
The following discusses using "ForbidDelMailbox" option.
2. For Exchange 2013 and for Microsoft's Office 365 tenant, mailboxes can preexist and be merged into by Migration Manager.