When we send out an invoice there is a custom automated email template and I want to edit/add to this email that sends the invoice, I cannot find the option to edit it.

Hi there, 

Welcome to the Community. QuickBooks provides the flexibility that allows you to edit the invoice email message. I'll glad to show you how below. 

Here are the steps:

1. Go to Account and settings in the gear icon.
2. Select Sales.
3. Click on the pencil icon in the Messages section.
4. From there you can start editing.
5. Click Done.

Give this a try and let me know how you make out. I'll be a message away in case you have other questions.