I do it all the time on the website. You click on make a payment, which shows you the combined billing amount. It gives you the option to pay the amount due or pay a different amount. If you want to pay more, just enter that amount and click next. The next page shows the breakdown of all your loans and tells you that you since you are paying an amount over the minimum due, you have to decide how it is allocated or leave it blank to have them do it for you.
Starting Score: April 2012 EQ 624