If you're not set up with QuickBooks Payments, you'll need to manually record the invoice payment in QuickBooks. Place it under Undeposited Funds to see it in the deposit window, and then transfer the funds to the correct bank by creating a bank deposit. Let me guide you through this process, @webstersllc
To begin with, let's record the invoice payment by following these steps:
- Click + New then choose Receive payment under the Customers column.
- Choose the customer's name from the Customer dropdown, or click Find by invoice no.
- Select the payment method from the Payment method dropdown
- From the Deposit to dropdown, choose the account into which the payment will go.
- In the Outstanding Transaction, select the checkbox for the invoice you're recording the payment for.
- Input the Reference no. and add a Memo if necessary.
- Click Save and Close to complete the process.

For further details on recording payments, you can check out this article: Record invoice payments in QuickBooks Online.
Next, let's record a bank deposit to transfer the funds to the appropriate bank. Here’s how:
- Select + New.
- Under the Other column, choose the Bank deposit.
- From the Account dropdown, choose the account you want to put the money into.
- Check the box beside each transaction you wish to combine.
- Ensure that the total amount of the selected transactions aligns with your deposit slip. Use your deposit slip for reference.
- Once verified, click Save and Close.

If you're using QuickBooks Payments and the payment hasn’t been deposited in your bank yet, the deposit process might still be underway. You can check the Deposits window to see if the payment has been posted. You can check this article: Find out when QuickBooks Payments deposits customer payments .
Additionally, it is crucial to reconcile your accounts regularly to ensure they match up with your actual bank and credit card statements. This helps maintain financial accuracy.
Lastly, if you need further assistance with your accounts and reports, consider our QuickBooks Live Expert Assisted service. This service provides guidance to help you make the most out of QuickBooks features, ensuring efficient and accurate management of your financial data.
Do not hesitate to reply to this post if you need further assistance with managing your payments here in QuickBooks. I'd be happy to assist you!