Student Loan Question

I was thinking I would set up weekly payments to apply toward the principal on a student loan and continue to make the regularly scheduled payment. I pay half and my son pays the other half. The payments were taken from our accounts prior to the due date. When we received the statement it reflected no payments and indicated we owed two payments and had late fees. I called and was told the system cannot handle partial payments and it takes the system time to combine the two partial payments and apply them as the monthly payment. I changed the date for both payments to be made on the same day nine days prior to the due date. I also set up a weekly payment to make principal payments. The statement reflected receiving this first payment and applied it to the interest. I called to find out how to designate this payment for the principle. I was told by the loan company that interest accrues daily and the payment would be used to pay off that. Is there anyway to make principal payments and avoid paying only the interest in this situation?