I'd be more than happy to share with you some insights and guidelines to help you have the easier way.
You can add the department as subcustomers in the main company so that you can do invoicing from there on. Then, you can utilize the class tracking feature for classifying the transactions. First, enable the class tracking option. Here's how:
- Open your company file.
- Go to the Edit menu, then select Preferences.
- Choose Accounting, then go to the Company Preferences tab.>
- Click the Use class tracking for transactions checkbox.
- Choose the Prompt to Assign Classes checkbox if you want a reminder when you haven't assigned a class.
- Pick OK.
You can use the steps in this link to assist you in creating your class list and categorizing transactions.: Set up and use class tracking in QuickBooks Desktop.
I'm adding this article you can use in the future: Filter, sort, or total reports by Class.
If you have any questions about any setup in QuickBooks Desktop, please leave a reply. I'll get back to you promptly. Have a great day!