Employee purchased products and repaid through a payroll deduction. How do I apply the payment? Do I have to do a journal entry?

You don't need to make a journal entry for the payment, Robert. Let me help you apply the payroll deduction.

To add the deductions, let's follow the steps below:

1. Go to Payroll, then Employees.
2. Click the employee you want to add the deduction to.
3. From Deductions & contributions, click Start or Edit.
4. From the Deduction/contribution ▼ dropdown, select + Add deduction/contribution.
5. From the Deduction/contribution type. Select Other Deduction.
6. Then, from Type, select Other after tax deductions.
7. Add a Description. This will be the deduction or product name. It will appear on paychecks.
8. Select how your deduction is calculated. Then, enter the amount or percentage.
9. Finally, Select Save and Done.

You can also set up pre-tax or after-tax deduction items and delete a payroll deduction item. This helpful article will expound more on this process. Please feel free to check it out: Set up, change, or delete employee-paid payroll deductions.

You might want to Set up, assign, and update a pay schedule in the future. This reference will guide you on how: Set up and manage payroll schedules.

You can always comment on this thread if you need further assistance recording payroll deductions. I'll be on the lookout. Have a great day.

@robertflewis441- 

Another option, you can us a free billing management app to sync with QBO. You can pay your business reimbursement to employees with check or ACH from your bank account. You can separate the expense from payroll transactions.