if you're character is male than you should get her automatically after leaving the telos academy. after you look at the recording of your trial, the handmaiden should come in and say that those are atris's records.
i fail to understand how anyone could have trouble on malachor v. the greater storm beast was easy, all the sith in the academy were easy, sion was easy, in fact the only part i had a little trouble on was against kreia's three lightsabers.
but those crystals were added content, because they were added to the game after the orignal version was released. if the pc version had been released at the same time as the xbox version than those crystals would not have been part of the game. they were added to the game, which is why they are only available through xbox live on the xbox version.
if you've ever role played using the d20 system than it would be a lot easier to understand. basically everything you do comes down to the roll of a 20 sided die plus your ability modifier