Before the 2016 release, you would set the ‘From’ field in the email template itself. You could chose a specific user, or select from merge options (Record Owner, Current User). In the new template interface, that field isn’t there anymore, so where do you define who the email is from when sending an email with a template? … well it depends on how you’re sending it…
If you use workflow to send it, the From field can now be found in the Alert definition, just below the template selection:
If you’re sending it via the zoho email client, as before, you use the dropdown (present only if you have multiple email addresses associated with your account.