Certain folder names can be skipped using the WellKnownFoldersToSkip parameters specified in https://support.quest.com/technical-documents/migration-manager-for-exchange/8.13/user-guide/configuring-migration-using-powershell
The complete list of folders that can be specified in the list is:
Contacts, DeletedItems, Drafts, Inbox, Journal, Notes, Outbox, SentItems, Tasks, MsgFolderRoot, JunkEmail, SyncIssues, Conflicts, LocalFailures, ServerFailures, RecipientCache, and CommonViews.
Currently Migration Manager provides no mechanism for skipping any other folders from mail synchronization collections. As an alternate approach Messages can be filtered through message classes using the following KB https://support.quest.com/migration-manager-for-exchange/kb/136065