This article explains how to manually charge an invoice with GoCardless (not automated payment).
Go to the relevant Customer
Click on the "Invoices" tab
Select the invoices you want to charge
Click on "Charge customer"
Select the account and adjust the amounts for partial payments
Click on "Charge now". When successful, the invoices' status will change to "Payment scheduled".
Please note that GoCardless payments take several days to settle.