Head to Tools > Integrations > GoCardless > Settings.
Tick the check-box next to the Automatic payment requests when mandate available text. Click on the Save button to complete.
Once enabled this setting will check if the customer has any active mandates. The system will then apply payment from these mandates to any existing invoices which have an amount less than that of the mandate. The system will also apply payment from active mandates to any invoices created in future with amounts less than that of the mandate.