Ok, so I've been lurking for some time and finally had to sign up to jump in on this. As a local of Bishop, I know the people who work in the permit office and as Steve C said, they care and do their best. To assume otherwise is to miss the opportunity these folks can offer in knowledge and assistance. But there are rules and regulations so just remember, they can't always wave a magic wand to solve issues. The Inyo and Rec.gov site may be convoluted at times, but there is a lot of information they are trying to put out and they can't put in bold lettering everything that someone might miss. While it doesn't help now Sara, there are two places I found that indicate a permit is good for the entire trip along with other FAQ and Whitney regulations that may be useful for future dates. Rec.gov defaults to one night out but provides a drop down menu to extend the date. I would also not recommend trying to go up without a permit for your friend, I've stopped and talked with rangers up there, they will check permits even if others say they've managed to avoid them.
Rec.gov Whitney Rules and Regulations FS FAQ for Whitney Permits