Customer paid an invoice via bank transfer, payment was received and applied to the invoice but never entered in the bank register (merchant sync'd with QBO).

I appreciate the screenshot you've provided, @Meisroofing.

I recognized how important it is to process your receivables efficiently. Rest assured I'm here to impart some details about how QuickBooks Payments process your deposits. 

When setting up QuickBooks Payments, you're required to select a default account where the funds will be deposited. Thus, the option to choose an account when recording an invoice payment isn't visible as it will be place automatically to that account. 

Moreover, you can always change the account where QuickBooks deposits the payments. You can go to your Account and settings and made some modifications. There, you can also verify if you've connected your account to QuickBooks Payment. I'll show you how:
 

1. Go to the Gear icon in your QuickBooks Online (QBO) and select Account and settings.
2. Click the Payments tab. 
3. In the Deposits section next to Standard Deposits, select Change bank.
4. Select Add new bank account.
5. Enter the needed details and select Save when ready.
6. Review the details and ensure it’s accurate before completing your request.

You can also see this article for more details: Change the account QuickBooks deposits payments info.

If this is not the case, I propose contacting our merchant support team. They'll be able to securely check your account and look into the reason why you're unable to select an account when recording a payment. 

In addition, I'm adding these links that you can read for reference. This provides details on how QuickBooks Payments process your receivables and how to match your accounts:
 

• Take and process payments with QuickBooks Payments
• Reconcile an account in QuickBooks Online

You can count on me if you need further assistance with your deposits. I'll be more than happy to help and work with you again. Keep safe!

It is set up to the right account, this has all been done. What happened is the invoice was sent to customer, customer paid via echeck, payment went through my quickbooks payment  merchant account and was sent to the customers invoice in quickbooks online showing payment received and applied to the invoice. I see the payment posted, but when it was funded/batched or deposited whatever you want to call it, Quickbooks online didn't finish the process of depositing the money into our bank account (as I have properly set up in the settings which is what you told me to do but was already done).  Somewhere when this funded and deposited Quickbooks online has a glitch and didn't process it properly.  Because when a customer pays via echeck or credit card it clearly states that I do not need to do anything, correct ??????  There is no data entry required to enter this payment, right???????????   QBO didn't record the deposit when this was batched and put into our bank account, if I go to undeposited funds it's sitting in there with no other side to it going into our Checking account.  There are 2 sides to every accounting transaction, there is only 1 part of this transaction going into undeposited funds, but it's not coming out and into our bank.  Undeposited funds is basically a wash account it should never have money being held in there, what that is what has happened to 7 of my deposits from my merchant account.  Who do I need to talk to about this?  And, I need someone other than the contact us button on your support process, I know more then them and they're just looking stuff up out of a book or asking a supervisor and I'm on the phone for hours with no resolution.  Sorry but QBO has many glitches and no one that I have talked to in tech support is savvy enough to deal with it!!   BEYOND FRUSTRATED WITH QBO GLITCHES, THERE ARE MANY!!!!

Thanks for taking the time to share all the details of your QuickBooks Payments concern, @Meisroofing,

I want to make sure this Merchant funds deposit concern is addressed properly.

For now, account specific concerns related to money movement is mainly handled by our Live Support Team. We're currently unable to trace funds or check your Payments account in this public forum for security reasons.

You can contact our Payments Support directly to trace the funds for you. To get a live rep to help you, click the following link for our contact details: Contact Payments Support

To share some insights about this, there are several reasons why posting of funds are delayed. The posting depends on the time when the transactions were created and which financial institution they are deposited. The period on how long it takes to verify and process electronic deposits may differ for each banks.

Additionally, there are instances when payments are taking longer than usual because the might be on hold for verification. For new QuickBooks Payments users, the first few payments take a bit longer to process while we set everything up. See this article to learn more about this: How long does it take to get customer payments into your bank account?

I want to make sure all your QuickBooks concerns are taken care of and I'm here if you need further help. Have a good one!