Thanks for reaching out to the QuickBooks Community, @wbsherlock.
Let me help share some insights on how you can assign different amounts of the salary to different jobs.
You can set up a billable timesheet so you can track payroll expenses by a job in your employee's paycheck. Right after, create an invoice for your customer and choose the billable time you set up for your employee.
Let's open first your employee's paycheck detail to add a Customer:Job (attached screenshot).
Now, let's set up a timesheet by following the steps below:
Once done, you can now create an invoice for your customer with the billable time. Let me walk you through the steps:
For additional reference, you can check these articles:
If you need further assistance with the steps, I recommend contacting our QuickBooks Desktop Support Team. They have the tools to pull up your account and do a remote session.
Here's how you can can contact our customer support:
That should do it! Feel me in if you have additional questions when creating timesheet and invoice. I'll be around to help you out.