If I have this right, the GoCardless payment has gone into the merchant account and the related invoice has been marked as paid.
I then upload a new statement, move the money out of my merchant account and tag it to the credit from Gocardless. This leaves a credit in the GC Merchant account and I apply a manual debit under bank charges.
Then how do I apply a tag to the original invoice or payment to code it as a deposit so it is not included for tax reasons?