This is a very common scenario in accounting, the guide here (which @Parker1090 kindly reference ) I’m sure will help:
Handling Payments from Merchant Accounts
The basic premise is that you have another bank account setup on Quick File called something like “GoCardless Merchant Account” (it may already have been automatically created). This is where you tag all your invoices payments to (not the current bank account). You then typically have a lump sum transfer (less fees) that GoCardless make to your current account, this is entered on the new GoCardless Merchant Account as a transfer to the current account. You will eventually accrue a balance on the merchant account which will match the fees deducted by GoCardless, you can enter a single “money out” transaction to balance this off and tag it to a supplier called something like “GoCardless charges”.
Hope that helps!