In my specific situation they are both flying on Virgin. I got their ticket info and pulled it up online, when you go to "view itinerary" there is a spot to add a FF#, but wondering if since the name for my account is different from the name of the person flying, if that will totally mess up their reservation...

I've used my miles to book flights for other people, and I've read in situations like using companion passes you would be credited the miles for the other passengers as well. And isn't that the whole point of business FF# accounts, that you earn points you buy for other people/employees? (I am trying to use just my personal account, but it seems to me if you could do it for the one, you could do it for the other?)