Upload Custom Automated Email Notifications

We can edit the email templates and upload for use on those emails that get sent from Sage CM by us, great. We ran into the problem as we were customizing, some of the templates, such as "ITB_PrivateMesage", could not be uploaded back into the system for use. This is because the email/template is sent automatically via TeamLink. If there could be a way to upload these types of templates back into the system for usage, that would be awesome. It is important that our documentation looks uniform and clean for our company.