You dont have to start a new game. It just takes effect when you put them in your "Override" folder in the KotOR II Directory. You may have to make it though.
I think that if you have a regular lightsaber in the main weapon hand, and a short lightsaber in the other hand, or "off-hand", you may get some sort of combat bonus. It reduces some penelty I think. If you have a regular saber in both hands, then it will either increase the penelty, or it wont change as opposed to having a regular saber and a short saber.
Ok, heres the deal: every time I try to either start a new game, or load a saved one, when it is loading I get an error message saying that it has to close. I have downloaded many mods, but they all work, and this has never happened before. Any help will be greatly appreciated.