In the process of wanting to add a new dynamic value, based on a customer account, into the invoice email that is sent out when a customer buys something from the store, it became evident that understanding of transactional emails would be needed.
To view Transactional Emails it is possible to to into the Magento backend System -> Transactional Emails. Within this section it is possible to create a new template based on the templates defined in the file structure.
Having defined a template in the previous section, it is then possible to associate that template to an action. This is done in the Magento backend System -> Configuration -> Sales (Sales Emails).