I have read that you can refine your personal crystal once you get it. How do you do that?

take it off your lightsaber and talk to kreia

after asking Kreia about it only a half dozen times or so or levelling up a few times she asks me to unequip the crystal from my saber and then she gives it back and you get a popup saying your pc crystal was upgraded

What does Kreia do to it?

She explains exactly what she does to it in the game. She aligns it to you.

You don't even have to lvl up. Just a simple change in alignment changes the crystals properties.

and she has realigned my crystal at least two or three times now, but to tell the truth I really don't know what it does.

Depending on you class and alignment, the crystal gives you a bonus in differnt skills. If you go to a workbench and choose to upgrade your lightsabre, simply highlight(don't choose) your crystal, and at the bottom of the screen, it will tell you what the bonus is for it.

Sometimes though it is a mistake to have your crystal realigned. For example, if you are max darkside or lightside and then you accidently fall a few points in the other direction, if you have Kreia realign the crystal it will be less powerful.