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Buy nowYou can use "Routines for QuickBooks" at the QB Labs. This will allow you to customize the Payment Receipt Email template. And also automatically notify your customers when you receive their payment. With this feature, there is no need to use manual "Save and send" to notify payment receipt to your customers. But I also think this newly added Save and send message template should be customizable (currently Intuit hard wired).
To turn on Routines for QuickBooks at the QB Labs:
Gear > Your Company > QuickBooks Labs.
To set up Manage Routines to notify your customers when you receive their payment.:
Gear > Tools > Manage Routines > Select Notify your customers when you receive their payment > Click Try It Out