Let's work together and link the payment to your invoice in QuickBooks Online. In your case, when receiving the invoice payment, it should deposit on the Undeposited Funds.
Here's how:
In the left menu,Sales.
Go to theInvoicestab.
Locate the invoice.
From theActionscolumn, click theReceive Paymentslink.
Make sure to chooseUndeposited Fundsin theDeposit Todrop-down.
Enter the full payment of the invoice.
ClickSave and Close.
Then, make a bank deposit and choose the bank account into which the actual payment was deposited.
Click the New (+) button in the left menu.
Select Bank Deposit.
Choose the bank account into which the actual payment was deposited.
Enter the date that the deposit was made.
Mark the invoice payment that has been paid in the Select the payments included in this deposit section.
Examine the payment information. The data should be identical to the downloaded bank transactions.
Please know that the Community and I are available to assist you with your income-related transactions. If you have any further questions, please return to this page. I'm always willing to assist.