The Chapter 13 Trustee strongly prefers that plan payment be paid through a payroll deduction; that way a debtor does not have to remember to send payments. If a payroll deduction is not desired, you can ask the trustee to make payment direct if you have a strong basis for it, e.g., you are in management and a payroll deduction might hinder workplace advancement.
If you are authorized to make direct payments, you will have to make payments through the TFS payment system. If you miss a plan payment, do not be surprised if the Chapter 13 Trustee sends your employer a payroll deduction request.