Typically, when dealing with credit card sales from your Shopify store, it's common to use a separate QuickBooks bank account and treat it as a “clearing” account to "hold" payments for orders from your Shopify store - and then transfer them into your QuickBooks “Bank” account as soon as they're deposited in your bank account in real life.
Using a clearing account in QuickBooks
This can be easily set up by creating a separate Bank Account in QuickBooks to act as a holding account for funds until they're deposited into your physical bank account by your card processor. This can be called "Shopify Clearing Account", for example.
Then, in MyWorks Sync > Map > Payment Methods, this account should be chosen as the account for MyWorks to sync orders to. If you have multiple payment methods in Shopify, like PayPal or Authorize.net, for example - you could create one clearing account for each payment method in QuickBooks to keep them separated!
Orders will then be synced into this bank account in QuickBooks, and when the deposit clears your bank account in real life, it would be "Transferred" from this holding account.
This results in your "clearing" account having a balance of only the sales/funds that have not yet cleared your bank account in real life: the amount that's still “on its way” to your bank from Shopify or your payment processor.
Transaction Fee Handling
Transaction fees can also be easily accounted for in this process by enabling transaction fees to sync as a line item in your orders in MyWorks Sync >Map > Payment Methods. By enabling this, the order totals in QuickBooks will represent the “net” amount you'd receive after fees, and would correctly record your transaction fees in QuickBooks without any extra effort on your end.