Our QuickBooks Desktop Sync for WooCommerce supports syncing orders to QuickBooks as either:
Invoice (and a Payment)
Sales Receipt
Estimate
Sales Order
Invoice + Sales Order (and payment, if applicable)
This setting can be changed in MyWorks Sync > Settings > Order tab.
If you are unsure which option to check, the best method is to consult your accountant on their recommendation - and/or check your existing QuickBooks Desktop company to see how you've been accounting for orders up to this point: whether as a sales order, sales receipt, or an invoice + payment.
The best method to determine which format to use is by answering the following question:
Do all the gateways in your WooCommerce store collect payment as soon as the order is placed?
Yes. You should sync orders over to QuickBooks as Sales Receipts.
No. You should sync orders over to QuickBooks as Invoices + Payments.
I use Sales Orders in QuickBooks. You should sync orders over to QuickBooks as Sales Orders.
I use Estimates in QuickBooks. You should sync orders over to QuickBooks as Estimates.
You can also opt to sync a Sales Order to QuickBooks as ADDITIONAL to the Invoice & Payment/ Sales Receipt MyWorks Sync would already sync to QuickBooks:
Here are the main differences between sales receipts and invoices.
Orders as Sales Receipts
A Sales Receipt is an invoice + a payment all rolled into one. Therefore, syncing an order as a sales receipt will record the sale and deposit the payment into the correct (mapped) bank account in QuickBooks Desktop. This is usually a typical representation of a WooCommerce order - where the order is placed and paid for all at once. The only exception would be someone paying for a WooCommerce order with a Bank Transfer or Cash on Delivery type of gateway - where the payment isn't received at the time of order.
Remember that if an order is placed with a Bank Transfer gateway, for example - the sales receipt in QuickBooks Desktop would reflect that payment has been received when in fact, it has not.
Orders as an Invoice + Payment
An invoice in QuickBooks Desktop represents a sale you've made that hasn't yet been paid. It's displayed in QuickBooks Desktop as "Open" until payment is added to the invoice. Therefore, syncing a WooCommerce order as an invoice + payment is perfectly acceptable. When the order is placed, it's synced to QuickBooks Desktop immediately as an invoice.
If the order was paid with a legitimate gateway in WooCommerce (aka Stripe, Authorize.net, PayPal, etc) - a payment for the invoice will be immediately synced over to QuickBooks Desktop to close out the invoice.
Otherwise, the payment will not be synced over - and the invoice will accurately remain as open in QuickBooks Desktop. Read more about syncing over payments for these types of gateways here.