Freight claims by customers on previously paid invoices are offset against current payment

Let me guide you on how you can record the deposit, Josephine5.

Generally, recording a customer credit or refund is done using a credit memo. This is one way to handle claims or offset against any payment. You'll want to record the transaction by following the steps to record bank fees in QuickBooks Desktop. To do so, you can follow the steps provided below:

1. Go to the Banking menu on the upper part. 
2. From the top of the application window, click Use Register.
3. Click the bank account for which you want to record a fee from the pull-down menu and click Okay.
4. Enter the date of the bank fee.
5. Type the amount of the bank fee in the Payment field.
6. Click Bank Services Charges from the Account pull-down menu.
7. Click Record to finish entering the fee and save.

This should now offset the amount from your current payment. However, I would also suggest reaching out to your accountant for the best way how to record the deposit. 

Additionally, QuickBooks Desktop offers a wide range variety of reports to cater to your business need. Learn how to customize them to get the data you need: Customize Reports In QuickBooks Desktop.

Feel free to let me know if you have any questions about offsetting your current payments. I'll always be here to help.

The answer supplied is not what we were hoping for.

This still does not relate the freight claims to a deposit for ease of reconciling cash.  It also doesn't connect the freight claims with a customer.  We were looking for a way to post the deposit intact with the freight claims as a deduction against the current invoices being paid.  Is there some way to create a credit memo or something else that can be posted in one entry with the invoices?

I’ll chime in on this thread to assist you further, @Josephine5.

Let me ensure you can offset the freight claimed by your customer against the current payment to their open invoices in QuickBooks Desktop (QBDT).

There are two ways I can share to enable you to get the result you wanted regarding your concern. First, we can create a service item for the freight claims and map this to an expense account. This way, we can add this one and enter the amount in negative to the open invoice. Then, the amount will be offset against the total amount of the invoice.

To add this as a service item, you can follow the steps below:

1. Go to the Lists menu and select Item List.
2. At to bottom of the window, click the Item dropdown and tap New. Then, select New Item.
3. Select an item type and choose Expense under the Account field.
4. Finish the setup by filling out the item fields.
5. Press the OK button.
   

Once done, go to the specific invoice and add this to another line item. Please make sure to enter the amount in negative.

On the other hand, you can collate all the amount paid for that specific invoice and deposit it to Undeposited Funds. Afterward, create a Bank Deposit for the following payments and add the expense account under the From Account field to diminish the freight claims amount. Let me walk you through the following:

1. Go to the Banking menu and select Make Deposits.
2. From the Payments to Deposit window, select all the deposits made for that invoice.
3. Then, add the expense account under the From account field, where you map the freight claim item.
4. Add the amount in a negative, then click Save & Close.
   

That should solve this matter, Josephine5. Additionally, I added this article for your reference when reconciling your account. This is to ensure that your books are balanced and enable you to review any discrepancies that might occur: Reconcile an account in QuickBooks Desktop.

Keep in touch if you have more questions about offsetting transactions. I’ll make sure to get back to assist your further. Have a good one!