Run the XenApp 6 Migration Tool cmdlets from the PowerShell console.
You can specify a remote server name; this is the name of the server in the legacy farm from which objects will be migrated. Specifying the remote server name as a migration option eliminates having to specify it each time you start a migration.
You can also optionally specify a nondefault folder location where the exported data from the legacy farm is stored, and object types or named objects to include or exclude from the migration.
Subsequent migrations (using the Start-XAMigration cmdlet) will use the current specifications in the server mappings, migration options, and property value overrides file.