When you choose the option of automatic payments through payroll deduction or any type of automatic deposits (Government payments, pension deposits, auto deposits from any outside account) an amount to cover the payment is held in your savings (or checking) account for each payment. So, for example, if your payment is $200 per month and you get paid weekly, $50 will be held in the selected account each week for the payment. If there is 5 weeks the extra $50 is accessible to you in your account. If you are paid bi-weekly $100 will be held per pay period, again in the event of an extra pay period the extra remains in your account.
This takes the worry out of making your payments as the money is set aside for you and the payment is automatically transferred to the loan.