Yes, there are two options on how you can track them separately, aimee-braley.
You can indicate it in the Memo section of the invoice to track if it's for an internal or external billing.
Aside from that, you can also use the Class Tracking feature in QBO. You can use this to get deeper insights into your sales, expenses, or profitability for each part of your business. Once you turn this on, you can assign classes to transactions.
One done, create a class for internal and external billing. Here's how:
After creating them, assign the class in the drop-down list for Class.
You can also check out these articles on how you can effectively use this feature in QBO:
I'll be around if you need more help when creating or tracking your sales transactions.