You can only save one template for each type of automated email (submission confirmation, acceptance notification etc) per CFP.
When you use a template, for example when accepting a submission, you are presented with a screen to enable you to make any ‘one off’ changes required for that particular submitter.
This feature is coming soon! In the meantime, you can use the “nudge draft submitters” feature, or send a one-off bulk email to selected (or all) submitters.