Not sure what you mean. When you setup online bill pay at Discover, you need to input your bank (PNC) and account number for the loan. Call PNC if you don't have the account # to setup bill pay with Discover, they'll be able to tell you if you just ask what account number you need to give to set up billpay with your other bank. Don't let them tell you that you have to use PNC's website, that's not true. The account number will ensure the payment gets directed to the loan account.
Now do you mean how will payments be allocated if you pay MORE than the minimum? In that case, you may have to give PNC a call and let them know whether you want the excess applied to principle directly to save interest over the life of the loan or to the next month's payment.
At least this is how I've always done Bill Pay personally. Maybe someone else can chime in if their experience is different.
