The following tutorial explains how payment methods such as credit cards and purchase orders interact with QuickBooks. A picture is worth a thousand words in this case.
As we can see, customers that do not have access to a profile giving them purchase orders or quote requests are presented with simple methods like credit cards, PayPal, and Amazon. When those orders are complete they download to QuickBooks (via UltraBooks) as a sales receipt.
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We also demonstrate quote requests in this flow. Quote requests are nothing more than an opportunity for the merchant to adjust pricing on large orders for wholesale customers. When the quote goes out to the customer, they ultimately flow back through the same workflow.