If your Shopify orders have partial payments or split payments, then choose to sync as ‘Invoice'. But if you receive 100% pre-paid payment for ALL your orders from your customers, then it is recommended to choose to sync as ‘Sales Receipt'.
We recommend all Pipemonk users to put the settings to sync as ‘Invoice’ to record Order Information in QuickBooks Online.
Invoices in QuickBooks Online support most of the complex needs warranted because of the accounting structure whereas Sales Receipt offers limited flexibility.
With Invoices, you can perform the following actions:
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Can track partial payments
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Link Journal Entry to an existing invoice
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Link credit notes and the corresponding payments to an invoice
For more details, about the Payment Transaction Fee check this article.