I read the guide CCNA made and its really good wow, but I searched and couldn't find a certain thing. When you update the ini files for multiple cores, should you enter 4 as the number if you have a quad core processor? I couldn't tell if you should only enter 2 no matter how many cores you have.

Only enter two cores, no matter how many you have. The reason for the .ini tweak is that Fallout 3 is not optimized to run on more than two cores, so the tweak forces it to only use two. This usually improves game stability quite a bit.