Delighted to hear again from you, @terrapindreamer.

I appreciate you for clarifying your concern and for providing additional details of it. Allow me to share some information on how you can achieve your goal.

With QuickBooks Desktop, you have the option to manage and keep track of your sales and accounts receivables both company wide and department level. You can add sub-customers to your list and send invoices and other forms to them. By doing so, you can keep track of each income, expense and balance for the company and each department. This is the same on how job costing works in the system.

Here's how:

1. Go to Customer.
2. Choose Customer Center.
3. Click Add New Customer.
4. Select New Customer.
5. Enter the company information.
6. Click Ok.

Now, let's add the sub-customer or the departments of the company. Here's how:

1. In the Customer center, highlight the name of the Parent Customer (name of the customer).
2. Click Add New Customer.
3. Select Add Job.
4. Type in the sub-customer's information.
5. Hit  Ok.

That should do it! Repeat the same process if you 'll need to add more sub-customers. 

Once you create an invoice, you'll be able select which sub-customer will it be sent.

Fill me in if you have other questions about creating and sending invoices to your customer. I’m always here to help.