Welcome to the Community, johnfilas.

Thank you for choosing QuickBooks Desktop as your partner accounting and tracking your payroll. I'm here to help set up a SEP IRA.

In a few easy steps, you can set up a SEP IRA. This item is used either for employee contribution to 408(k)(6) SEP or company contribution to an employee's 408(k)(6) retirement plans.

To do this task, please follow these steps:

1. Go to Lists and choose Payroll Item List.
2. Click on the Payroll Item drop down and select New.
3. Choose Custom Setup (allows editing of all settings; recommended for expert users) and click on Next.
4. Choose Deduction if this item will be used for employee contribution, enter a name, and select the name of the agency to which liability is paid. Then, choose 408(k)(6) SEP in the Tax tracking type window. 
5. Choose Company Contribution if this item will be used for company, enter a name, select the name of the agency to which liability is paid. Then, choose 408(k)(6) Co. Match in the Tax tracking type window. 
6. Select your option in the Calculate based on quantity window and click on Next.
7. Set your default rate and limit and click on Finish.

I've attached some screenshots below to help you with the process.

As a reference, you can refer to this article for further guidance: Set up a payroll item for retirement benefits (401(K), Simple IRA, etc.).

This should point you in the right direction. Let me know if you have further questions. I'm always here to help.