All deposits were directly entered into bank - how do I go back and correct?

Welcome and thank you for posting here in the Community, @dphillips21. I'll make sure that you can rid of the duplicates. 

When you record bank deposits, the transactions posted to the Undeposited Funds account will show up. These are the payments that must be combined into a single record in order for QuickBooks to match your bank records. 

You can open the Undeposited Funds account in your Chart of Accounts since these are duplicate entries. Then, from there, delete the transactions. Here's how to do it: 

1. Go to the Lists menu.
2. Choose Chart of Accounts.
3. Locate and then double-click the Undeposited Funds account to open it.
4. Find the duplicate transaction and right-click it.
5. Choose Delete Payment or Delete Deposit from the drop-down menu.
6. To confirm the changes, select OK.

I'm also adding this article to learn more about the different ways in tracking customer payments in QuickBooks Desktop: Get started with customer transaction workflows.

Feel welcome to leave a comment below if you need more help in handling your other transactions. I'm always here to back you up. 

Thank you for your response. When I delete the payments from Undeposited Funds, it doesn't change the double-counted income. Any help would be great!

Thank you.

I want to stop the duplicate payments issue from happening to your account, @dphillips21.

Thanks for following the suggested steps provided by my colleague above. Allow me to share details about paying customers and depositing funds in QuickBooks Desktop (QBDT). This way, I can guide you accordingly. 

The workflows of the paying client in QBDT are:

• Invoice → Payment →Deposit 
• Invoice → Payment- this will occur if you select a specific bank in the Deposit dropdown menu when you receive payments. 

The deposits and payments are normal when you follow the workflow. See screenshots below to see what transactions look like after following the workflow above:

For additional knowledge, click this link: Get started with customer transaction workflows in QBDT.

If your account is connected to your online banking, ensure to find a match. This way, the payments will not duplicate in the system. For more information, see this link: Add and match Bank Feed transactions in QBDT.

In addition, when you create a deposit in the bank register directly, this transaction will only appear on this page, not in the customer invoice lists. Since this is creating duplicates, we'll need to investigate your account in a safe place. With this, I'd recommend contacting our Customer Care Team.  

Here's how: 

1. Press F1 on your keyboard to open the Help page. 
2. Click Contact Us. 
3. Enter your concern in the box and select Continue. 
4. Choose either Start messaging or Get a callback. 
5. Complete the required data and submit the request.

Make sure to contact them within business hours to ensure a swift response.

Moreover, don't forget to reconcile your accounts regularly to make sure they match your real-life bank statements. 

Additionally, you can read these articles to know when you have to make a bank deposit and learn how it works in QuickBooks:

• Record and make bank deposits
• What are Bank Deposits in QuickBooks?

Don't hesitate to let me know if you have follow-up questions about your bank deposit transactions. I'm here to assist you every step of the way. Stay safe and have a wonderful day ahead, dphillips21.