Hey there, @smoorman,

Thanks for getting in touch with us today. I can share some insights about setting up a commission only employee in QuickBooks Desktop.

At the moment there isn't a way to auto-calculate the commission on your sales transaction and apply them to the employee's paychecks. You can, however, set up a commission item so you can automatically add it in the payroll check.

Here's how to create a commission item:

1. Go to the Lists menu.
2. Choose Payroll Item List.
3. Right-click anywhere and click New.
4. Choose Custom Setup.
5. Click Next.
6. Choose Wage in the Payroll item type window.
7. Click Next.
8. Select the Commission in the Wages screen. Click Next.
9. Enter the commission description then click Next.
10. Choose the Expense account.
11. Enter the commission rate.
12. Click Finish.

Once done, you can apply this item in the employee's profile. Here's how:

1. Click the Employees  menu.
2. Go to the Employee Center.
3. Double-click on the employee's name.
4. On the Payroll Info tab, add the item under Earnings by clicking in the white box under item name and choosing the item from the drop-down list.
5. Enter the rate in the Rate column.

Once done, you can now pay the employee's commission on his check.

When you create the paycheck, you should see the commission item in the Earnings section.  You must enter an amount in the Rate and Quantity columns to get the total commission amount.

That should get you on the right track. You can check out this article to know more about the process: Set up commission payroll item and reports

Please let me know if you have additional questions about your concern. I'm here to help you anytime, @smoorman.