Customer payments entered in error

http://support.quickbooks.intuit.com/support/Articles/HOW12342

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Correct customer payments that have been deposited and reconciled

You can move a payment that has been incorrectly applied from one customer to the correct customer, if the payment has already been deposited and reconciled.
You can also use this process to correct any customer payments that were entered through the make deposits screen and are not connected to an invoice.
Performing the following steps in QuickBooks will correct these issues and allow the reconciliation to remain intact.

Detailed Instructions

To correct a misapplied payment:

1. Create a duplicate payment for the correct customer:
   1. Select the Customers menu and select Receive Payments.
   2. Create a duplicate payment for the correct customer.
   3. Click Save & Close.
       
2. Delete the original payment and recreate payment line in (reconciled) deposit:
   1. Select the Banking menu and select Make Deposits.
   2. Click the Cancel button at the bottom of the Payments to Deposit window
   3. In the Make Deposits window, click the Previous button until you find the deposit containing the original payment (that was incorrectly applied).
   4. Click the Payments button at the top of the window to open the Payments to Deposit window again.
   5. Select the newly created payment and click OK to add it to the previously reconciled deposit.
   6. In the Make Deposits window, select the original payment.
   7. Select the Edit menu and select Delete Line.
   8. Click Save & Close to automatically replace the original payment with the new payment.
   9. Click Yes to the warning: "You have changed the transaction."
       
3. Delete the original payment.
   1. Select the Customers menu and select Receive Payments.
   2. In the Receive Payments window, click the Previous button until you find the original payment.
   3. Select the Edit menu and select Delete Payment.
   4. Click OK to the warning: "Are you sure you want to delete this transaction?"
   5. Click Save & Close.

The payment has now been applied correctly and the reconciliation left intact.

Correcting Deposits made through the register or through the Make Deposits window that were not applied to customer payments:

1. Find the deposit in the register
2. Double-click on the DEP line
3. Change the Received From line to Undeposited Funds
4. Click the Payments button on the top
5. Place a Check mark next to the payments that this deposit belongs to
6. Save and Close the deposit

The payment should now be correctly applied to the deposit.