Give them a call man, so far i never found anybody who accepts additional payments on principal only through online system. You usually have to call them and then write a check and write "PRINCIPAL ONLY" in the memo...Check what is the case with them by phone...
Thanks Ukimafija and everybody for their replies!
I would be happy if it is possible to pay the due payment and allocate all the extra payment to the principal without the need to call PenFed afterwards. This is the way I used to do with Chase because they allow it online. Now I have Ally auto loan and in order to allocate any extra amount over the minimum due, I have to call them which is really a hassle because sometimes they do it and sometimes they don't and then I have to call again until they fix it.