Personally, I wouldn't want to raise a batch invoice in my customer account as it would cause confusion and query with the customer.

We have a similar issue with Paypal.  When funds come in, we post the actual net amount as a bank transfer to the main bank account, then post a sales receipt for the full value that the customer paid, then a bank payment for the fees, all using the same "Ref" as the net £ amount received. These 3 transaction net to zero in the control account.

In one client situation there are only a few transactions a month so it's not too onerous, but another client has multiple payments a day so we now download reports showing actual receipts, fees and transfers and import that into Sage through 3rd party add ons.

Personally, I wouldn't want to raise a batch invoice in my customer account as it would cause confusion and query with the customer.

We have a similar issue with Paypal.  When funds come in, we post the actual net amount as a bank transfer to the main bank account, then post a sales receipt for the full value that the customer paid, then a bank payment for the fees, all using the same "Ref" as the net £ amount received. These 3 transaction net to zero in the control account.

In one client situation there are only a few transactions a month so it's not too onerous, but another client has multiple payments a day so we now download reports showing actual receipts, fees and transfers and import that into Sage through 3rd party add ons.