I looked at my checking register and noticed qb payment deposits (system recorded) for a customer is in un-deposited funds. The amount is in my checking account.

I can help you look into your register, Jennifer529.

After you process payments, QuickBooks puts the money in your bank account. It uses the bank account you picked when you signed up for QuickBooks Payments. We can check your payments setup into which account you selected. 

Also, if your balance is correct you can leave it as is. However, if it causes duplicates, it's possible that you created a manual payment and the deposit were not linked to an invoice. You can either delete the deposit or the manual payment you recorded and recreate the payment by linking the deposit to the invoice. 

For your reference, here is an article that can further guide you in handling customer payments in QuickBooks:

• Take and process payments in QuickBooks Online
• Deposit payments into the Undeposited Funds account in QuickBooks Online

lease let me know how it goes or if you have any other questions by leaving a comment below. I'm always here to help.