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Can I please confirm are these invoice's being created manually or are they for recurring transactions set up in QuickBooks Online?
These are recurring transactions in QuickBooks Online (the direct debit is handled by GoCardless who email a notification to the customer but not the actual invoice).
My thinking was to email the invoice prior to payment date, and that because it is paid by direct debit the invoice, and email, would clearly indicate this. But that doesn't seem to be the case.
You will need to create a separate invoice template for your recurring direct debit transactions, where you can set up a specific email to be sent when using that template - when you then set up the recurring invoice that is sent out, you can select this template.
To create a new invoice template, go to the cog wheel, custom form styles and then New Style. Once you have created your template, click on the Emails tab and type out the message you would like to be sent to your direct debit customers. Then, go to your recurring transactions under the cog wheel and edit the one you need - click on customise at the bottom and select the invoice template you have created.
Please let us know if you have any further questions.