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The simplest way to record your sale is to write an invoice for the commission. You can create a commission item, and on your invoice you can write the reference numbers of the credit card payments in the Description field of the line item. That way, your customers has a reference of what you're invoicing for.
On the bookkeeping side, it's best if you can seek advice from an accountant. You can ask if is it still necessary to include the credit card payments to your invoice and add a commission line to it, this may affect your sales tax. Or, you can just invoice them with the commission item.
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