First we need to write an email to send to your customers so go to
Contacts > Email > Emails
From here fill in the unique Email Code and Description
Ensure that you select your email in the Send From drop down menu
and then build the email you wish to send your customers who order a subscription
To set the email specifically for your subscription orders go to
Orders > Settings > Automatic Processing Controls
In the Details tab set a Description
Under the conditions tab trigger it if "Contains product in category" and select your category for your subscriptions from the drop down menu.
Then in the Actions tab under Send Customer Email select the email you set up from the drop down menu
You may also want to use the "Set order status" drop down so these don't clutter up your orders dashboard with subscription orders that don't require attention.