Amazon Store Payment Setup

We are going to experiment with setting up an Amazon Pro Merchant store. If it's successful, we'll have to integrate with Netsuite. But, since we are just evaluating it initially, we need to set up a manual means of entering sales orders and accepting payments. We will be using an invoice to capture the order with each individual customer.

The dilemma is how to accept payments from Amazon and apply them to the correct customer invoices while "deducting" the Amazon sales commission in the most efficient method.

Has anyone tried this yet? Any thoughts on how to best implement? Short of having Amazon as the customer, I haven't come up with an epiphany on how to simplify this since all Netsuite payments need to be applied by customer and there is no obvious way to deal with the Amazon sale commission they take out.