Thanks for coming back and providing us with in-depth details of your concern, Al252.

It could be there might be an issue with the way the transactions are being recorded in QuickBooks Desktop. When receiving a payment from a customer, we need to record it against the invoice and choose to deposit it into "Undeposited Funds." This keeps the payment in a holding account until you are ready to group it with other payments and deposit them all to the bank at once.

In your case, the payment may have been recorded in the bank register as well. This is why you see duplicate and incorrect deductions from your bank balance. To correct this, we can delete the incorrect entries from your bank account register. Let me guide you on how: 

1. Go to your bank account and register in QuickBooks Desktop.
2. Find the duplicate or incorrect transaction that shows the invoice amount deducted.
3. Right-click the transaction and select "Delete" or choose the transaction and click "Edit > Delete" from the menu.

After you've deleted the incorrect transaction, we can properly deposit the funds. Let me guide you on how: 

1. On the Homepage, select Record Deposits / Make Deposits.
2. In the Payments to Deposit window, choose the payments you want to combine. Then click OK.
3. Select the account you want to deposit from the Deposit to drop down in the Make Deposits window.
4. Check the deposit total. Make sure the account and selected payments match the deposit slip from your bank. Use your deposit slip as a reference.
5. Enter the date you deposited at your bank.
6. Add a memo as needed.
7. When you're done, press Save & Close.

From there, all payments in the Undeposited Funds account will automatically appear in the Bank Deposit window. You can check out this article for more details: Deposit payments into the Undeposited Funds account in the QuickBooks Desktop.

Once done, check your bank account register again. The bank balance should now correctly reflect the deposit without duplicated entries.

Moreover, you can refer to this article on how to track customer transactions in QuickBooks Desktop: Get started with customer transaction workflows in QuickBooks Desktop.

We are always here to help if you have any other concerns or questions about bank deposits or any QuickBooks-related concerns. You have a good one, Al252.