Tagging GoCardless?

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?

This looks broadly correct, although I don’t understand your last statement?

Presumably your income from GoCardless is related to your business and should be used to calculate your profits and resulting tax liability.

If you search the forum for GoCardless there are quite a few posts on how to reconcile your GoCardless accounts, here’s one to get you started.