Hi there, kbolton.

QuickBooks will match the transactions if they have the same amount. It's also considered a Match if the transaction date is within 90 days. Since the imported imported transaction is different from the what's recorded in QuickBooks, it will be not considered it as a match.

You might want to post the Sales Receipt in the Undeposited Funds first. Then, follow the same steps I've shared above to record the merchant or Shopify fee in making a deposit to the bank. Once done, use the deposit in looking for a match. 

I will also forward your feedback and feature request to our product engineers. They will review this future updates. 

Visit us again in the Community if you have other questions.