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In EM12c, go to the 'Enterprise' menu, then 'Job', then 'Library'. There should be an out-of-the-box job called "DISABLE TABLESPACE USED (%) ALERTS FOR UNDO AND TEMP TABLESPACES" that you can run against your database targets, and that job will disable database-generated alerts.
If a previous admin has set up EM12c-generated alerts for undo and temp, then yes, a monitoring template will take care of disabling them. Either remove those alerts from the existing monitoring template and apply them to your targets, or create a new monitoring template based on one database's current settings, remove those warning/critical thresholds for your undo and temp tablespaces, and apply it to your targets.