1. Set the "Lead Notification Brand" to your agency brand (Adminstration->Account Settings) on your client account.  All lead notifications that are sent using a template that is 'linked' to a system template or one of the email templates in your agency master account, will use this brand.
  2. Create your own lead notification templates in your agency account under Assets => Email Template Library.  Set the brand of the template to your agency brand.  
  3. Link to these templates in your client workflows by replacing existing Email Sales/Marketing workflow actions with a new action. When creating the new action, choose one of your agency templates and 'link' to the template.