Hello there, A Notary Company.
QuickBooks Online uses the date and amount when matching transactions. Thus, the check number isn't an option when matching. Also, bill payments only have reference number but don't have check number.
As a workaround, you can open the possible matches to verify if which of them is the correct match.
You'll want to contact our Customer Care team, kindly follow the steps below:
Feel free to post again if you have more questions.