Custom assets.
Don't alter your core game files. Just copy any file you intend to mod into your custom assets folder, and modify the files in your custom assets. Custom assets are loaded on game start up automatically so your game will play with any changes you make there, but that way you still have the originals in the right place so you wol't permanently flub up your main civ4 files. And trust me, you'll mess something up while modding, it's inevitable.