Shopify and Quickbooks Sales Reciepts

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Does anyone know how to properly sync Shopify Sales with Quickbooks? We are running into an issue with using the Quickbooks Application to link Shopify Sales over to our Quickbooks Online system. All purchases, even if they are made on account, are sent over as Sales Receipts with positive payments, with the Payment Method just reflected as "On Account". Has anyone found a solution to this via Shopify or Quickbooks? 

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I've been thinking of signing up with Quickbooks so this doesn't bode well. Following
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