Not familiar with Penfed, or their Loan policies. However, most Loans should have the option to pay down the principle by paying any amount over your regular payment. On rare occasion though some Lenders will not as they want all that interest, which is why they loaned the Money.
Loan payment is $325, you pay $1,325, and the $1K over should be applied to the principle.
Personally I would just call them and dicuss the issue, and how it works there. Some banks require you to call in to make principle payments.
I agree if it is ONE loan usually an amount over goes to the Principal but some places like stated do require you call to make those type of payments or you have to make them a seperate way. If it is a Few and you are trying to apply principal to a specific one sometimes they require you to set up which one you want the principal to apply to if you pay over the payment otherwise it may go to all of them evenly.
PenFed REQUIRES you to call customer service in order to realize payments above your monthly payment amount. I.E. principal only payments.
You may just have to call in, as it could vary by company.
My CU doesn't allow principal payments online, I have to go into the branch or call in to get it done.
I had an autoloan in the past where I had to send in a separate payment. It's just YMMV with banks.