Hi Zappy,
Thanks for posting. It seems like your client got an advance payment from Shopify, which will be taken from their future sales. The net amount, which is the total sales minus the advance, is what should show up in the bank.
When they receive a full payment from a customer that includes an overpayment, just enter it as is. MYOB will automatically make a credit for the extra amount. You can then either refund this extra amount to the customer or use it for one of their other unpaid invoices.
To make sure everything is correct, you'll need to check that the net amount in your client's bank account matches the same amount in their Shopify account. If these amounts are the same, then everything is good. For more detailed instructions, you can refer to this article about the customer payment and reconciliation process.
Feel free to post again anytime you require further assistance.
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Kind regards,
Shella