This is a very quick guide to setup Drupal Commerce order confirmation emails using Commerce_Message as there seems to be a lack of knowledge regarding this modules capabilities.
The various admin paths you should be looking at:
Edit the commerce_message order confirmation email [Commerce_message already installed]:
admin/structure/messages/manage/commerce_order_order_confirmation
You can clone this message and edit the clone as required or just edit it directly
Commerce_message provide its own versions of the Drupal Commerce tokens. e.g. [message:message-commerce-order:commerce-customer-billing:commerce_customer_address]. Look at the bottom of the confirmation order message edit page for the very long list of commerce_message tokens.
Edit the commerce_message order confirmation email rule [rules already installed]:
admin/config/workflow/rules
search for the rule rules_commerce_order_message_order_notification
You can clone this rule and edit the clone as required or just edit it directly.