I have a similar situation (online sales and merchant fees being deducted from the deposit) and have an additional question. When I go to receive payment the sales receipt does not show up. I verified the sales receipt has undeposited funds as the deposit to. I assume it is not showing up under receive payments because a sales receipt is assumed an automatic payment, therefore it is already showing up as paid. So how I do I work around this? I don't want to have to delete a sales receipt and create an invoice ever time a sale occurs. This is a ridiculous inefficiency in this day and age.
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