The basic idea is that you have a dummy bank account that represents GoCardless - you mark your customers’ invoices as paid in full into the merchant account, the payouts that you receive are transfers from the merchant account to your current account, and the difference (their fees) is accounted for as an expense paid from the merchant account to balance things up.
The “payment from a customer” happens when GC collects the direct debit, not when they send the net settlement to you.