That's the only way. Basically, any extra is automatically applied to future payments. Unless there's something specifically in the memo they'll play stupid. The checks are electronically scanned/deposited.
I did the pay/call dance with them for a year. Thought payments were bringing down principle and Sallie-Mae kept pushing mack my due date. Called every month to have the account adjusted and took great pleasure in feeling their annoyance.
Starting Score: 675