Can direct debit invoices have a custom email message which make it clear that payment is via direct debit instead of the standard message which asks for prompt payment?
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.